Keto Diet Risks Are Varied, Multiple Studies Show (2025)
Story at-a-glance
- A ketogenic diet improves weight loss, insulin sensitivity, and blood sugar control initially, but these gains typically level off after six to 12 months of adherence.
- Long-term keto can elevate low-density lipoprotein (LDL) cholesterol levels, particularly during rapid weight loss, raising cardiovascular concerns especially in healthy young adults following this diet
- Restricting carbohydrates eliminates healthy fruits, vegetables, and whole grains, leading to deficiencies in essential vitamins (B-complex, A, E, K) and minerals like magnesium and potassium
- Extended ketogenic diet use increases risks of kidney stones, reduced bone mineral density, thyroid dysfunction, and harmful gut microbiome changes linked to cancer risk.
- The keto diet works better as a short-term therapeutic strategy for metabolic inflexibility and diabetes, but requires transitioning to balanced carbohydrate intake for long-term health.
What Do New Studies Say About Keto’s Long-Term Safety and Efficacy?
In a study published in Science Advances, researchers paint a different picture contrary to the mainstream view of the ketogenic diet. Specifically, its long-term safety and metabolic effects are still under investigation, with growing evidence suggesting both promise and potential pitfalls:1
•The research affirms the short-term benefits — Ketogenic diets consistently produce early improvements in body weight, insulin sensitivity, and glycemic control. However, the literature the researchers reviewed shows that these gains tend to level off after several months, and the sustainability of such changes depends heavily on adherence and nutrient quality.
Several long-term trials included in the paper note that after the first six to 12 months, weight loss plateaus, and metabolic markers may begin to shift in variable directions depending on the composition of the diet and the individual’s baseline metabolic health.
•One of the recurring themes is that the ketogenic diet’s effectiveness depends on the context — It works particularly well in individuals with insulin resistance or Type 2 diabetes, but the metabolic benefits are less clear in healthy populations. The study also noted that adherence rates in long-term studies are relatively low, highlighting that maintaining nutritional ketosis over extended periods can be difficult in real-world conditions.
•Long-term safety isn’t fully understood yet — Another important finding is that while ketogenic diets can improve key metabolic markers, they also trigger compensatory changes that blunt or reverse some of those benefits. In fact, certain health problems have already been recorded, as you’ll learn below.
How Does Keto Affect Insulin Resistance and Other Metabolic Markers?
The study goes into detail on how ketogenic diets influence insulin resistance and associated biomarkers:2
•HOMA-IR and insulin sensitivity — Ketogenic diets have been shown to lower fasting insulin levels significantly, reducing the homeostasis model assessment for insulin resistance (HOMA-IR) index, which measures insulin resistance.
The paper reports that in both obese and diabetic subjects, HOMA-IR improves substantially during the first months of ketosis. This improvement is largely attributed to the reduction in carbohydrate intake, which minimizes the need for insulin secretion and allows tissues to regain sensitivity to insulin.
However, the paper also warns that this improvement is not uniform across all individuals. In some of the studies reviewed by the team, insulin sensitivity initially improved but later reached a plateau or showed mixed results after extended ketosis. This variability is attributed to physiological adaptation, differences in macronutrient ratios, or the duration of adherence by the participants.
•Fasting glucose — The paper highlights consistent reductions in fasting glucose across several trials. Subjects on ketogenic diets typically exhibit lower baseline glucose values compared to those on higher-carbohydrate regimens. This effect is particularly strong among individuals with impaired glucose tolerance or Type 2 diabetes.
However, in some long-term interventions, fasting glucose levels tend to stabilize rather than continue to decline, suggesting a new metabolic steady state rather than ongoing improvement.
What Happens to Your Lipids on Keto?
Lipids are fatty compounds that travel throughout your body. They’re found in your cell membranes and play a role in what goes in and out of the cells. In addition, they transport nutrients and are used in the production of hormones.3 Within this context, what happens when your body has a high intake of fat?
•Increase in low-density lipoprotein (LDL) occurs — In a case study published in Cureus, a 56-year-old woman had already been on a ketogenic diet for 30 to 40 days (along with regular exercise) before approaching the research team due to fatigue complaints.4 After tests were administered, the team discovered that she had a rapid increase in LDL cholesterol, often referred to as the bad cholesterol.
•Factors contributing to rise in LDL cholesterol — Under the ketogenic diet, the subject lost weight, but the speed at which it happened caused unforeseen health problems:5
“The drastic elevation in her LDL-C could also be explained due to the rapid weight loss, as cholesterol in the adipose tissue is known to mobilize as the fat cells shrink. Interestingly, her BMI [body mass index] four weeks after the discontinuation of ketogenic diet did not change despite a marked improvement in her LDL-C.”•Other studies support the findings — In a 2021 paper published in Nutrients, researchers noted that following a ketogenic low-carbohydrate high-fat diet (LCHF) contributed to a rise in LDL cholesterol. Overall, they advise against following this eating pattern, especially on a long-term basis:6
“The data suggest that feeding healthy, young, normal-weight women a ketogenic LCHF diet induces a deleterious blood lipid profile. The elevated LDL cholesterol should be a cause for concern in young, healthy, normal-weight women following this kind of LCHF diet.”Do Animal Data Reveal Metabolic Risks You Should Care About?
Going back to the Science Advances study, the researchers drew on several animal studies to illuminate possible long-term metabolic risks associated with sustained ketosis. These findings provide mechanistic insight into what can occur in humans after prolonged adherence to a high-fat diet:7
•Animal data consistently show that ketogenic feeding alters lipid metabolism and mitochondrial function — Some rodent studies reviewed in the paper reveal hepatic lipid accumulation, suggesting that long-term ketosis may promote fatty liver changes in certain conditions. This outcome appears to depend on the fat type and overall energy intake, as not all studies report this effect.
•Changes in gut microbiota composition — In another study, researchers showed that the ketogenic diet reduces microbial diversity in both animal and human tests. Specifically, they noted that Bifidobacterium was affected, which, as I noted in a previous article, is important in maintaining the integrity of mucin in your gut:8
“We focused on Bifidobacterium which had a reproducible decrease in abundance during KD consumption in both humans and mice and also with feeding of a synthetic KE in mice. Changes in Bifidobacterium abundance resulted in a significant alteration to intestinal Th17 cell populations …In humans, both Fusobacteria and Escherichia were significantly enriched on the KD, which have both been implicated in predisposition to colorectal cancer.”
Where Do Safety Flags Appear?
In addition to the health effects of the keto diet discussed above, the ketogenic diet has been associated with other concerning issues. These include:
•Nutrient deficiencies — The ketogenic diet requires you to take out many carbohydrate-rich food sources, like whole fruits, vegetables, and certain whole grains, all of which are loaded with vital nutrients your body needs. As noted in a study published in Frontiers in Nutrition:9
“Low-carbohydrate diets are often low in thiamin, folate, vitamin A, vitamin E, vitamin B6, calcium, magnesium, iron, and potassium. In the absence of multivitamin supplements, individuals on low-carbohydrate diets are at risk of frank nutritional deficiencies.Even when consuming only nutrient-dense foods, a 4:1 ketogenic diet is reported to have multiple micronutrient ….”
•Kidney stones — The risk of kidney stones is highlighted as a consistent observation, especially in studies involving long-term ketogenic use. In a 2023 study, for example, 15 out of 88 epileptic children developed renal stones and had to take medication. Moreover, one of them required surgery.10
•Bone health and overall fitness — The ketogenic diet also raises concern about bone health. Although the mechanisms are unclear, even a short-term regimen can impact bone mineral density. As noted in a study published in 2020:11
“Our data reveal novel and robust evidence of acute and likely negative effects on the bone modeling/remodeling process in elite athletes after a short-term ketogenic LCHF diet, including increased marker of resorption (at rest and post-exercise) and decreased formation (at rest and across exercise), with only partial recovery of these effects following acute restoration of CHO [carbohydrate] availability.Long-term effects of such alterations remain unknown, but may be detrimental to bone mineral density (BMD) and bone strength, with major consequences to health and performance.”
•Thyroid function and body weight — In another study, following the ketogenic diet was noted to have a negative effect on thyroid function, which eventually lead to hormonal changes resulting in greater loss of lean body mass compared to those who ate a diet high in carbohydrates.12
How Can You Reduce Risks if You Still Choose Keto?
While I’ve highlighted the pitfalls of a ketogenic diet, remember that the devil is in the details. I don’t recommend dismissing it entirely, as it still has a place in achieving optimal health, particularly when it’s done safely and correctly.
•Short-term keto can still be applied — In my interview with Georgi Dinkov, we discussed that the ketogenic diet, when followed properly, can be useful for people who are metabolically inflexible. It’s only in long-term applications that you’ll run into health problems.
Your body requires glucose and depriving it from this fuel raises cortisol levels. Through a process called gluconeogenesis, cortisol breaks down your muscles, bones, and brain to create its own glucose levels — a likely explanation to the reduced bone and lean mass discussed in the studies earlier.
•Dietary recommendations — If you go on a short-term ketogenic diet, make sure your healthy fats come from nutritious sources, such as pasture-raised eggs, butter and wild-caught fish. In addition, minimize your intake of ultraprocessed foods, meats, and snacks.
It would be wise to keep a high-quality multivitamin supplement with you, too. As explained earlier, strictly following a ketogenic diet introduces nutritional deficiencies, and taking a supplement can mitigate these issues down the road.
•Eat more carbohydrates as time goes on — Listen to your body to know when your metabolic flexibility returns. This process can take anywhere from a few weeks to a few months, and when you reach this point, you’ll need to eat more carbohydrates. Again, this goes back to the cortisol-glucose connection.
What’s the Bottom Line for Your Metabolic Health?
Tying everything together, a short-term ketogenic diet can be a helpful tool for improving metabolic health, especially in the context of insulin resistance and Type 2 diabetes.
•However, the long-term picture is more complex — The same mechanisms that drive early benefits — reduced insulin resistance and elevated fat oxidation — introduce new physiological challenges when sustained indefinitely. Potential risks include nutrient deficiencies, renal strain, thyroid dysfunction, altered gut health, and lower bone mineral density.
•Don’t overdo the ketogenic diet — As I highlighted earlier, it would be wise to view the ketogenic diet as a temporary therapeutic dietary strategy, not necessarily a lifelong eating pattern. For long-term health maintenance, however, the studies clearly show that a high-fat diet isn’t sustainable, and that carbohydrates are needed for a balanced approach that creates metabolic flexibility.
Frequently Asked Questions (FAQs) About Following a Chronic Ketogenic Diet
Q: Is the keto diet safe long term?
A: The long-term safety of the ketogenic diet remains uncertain. While early studies affirm short-term benefits such as weight loss, improved insulin sensitivity, and better glycemic control, the article stresses that these effects tend to level off after six to twelve months.
Moreover, adherence is difficult, and researchers have observed metabolic adaptations — including changes in lipid metabolism, energy expenditure, and thyroid hormone activity — that reduce metabolic efficiency or alter endocrine balance over time.
Q: What are the common side effects of the keto diet?
A: There are several safety concerns and side effects that arise with prolonged ketogenic eating:
•Nutrient gaps — By removing many healthy carbohydrate foods, keto can cause deficiencies in vitamins (B-complex, A, E, C, K) and minerals such as magnesium, potassium, calcium, and iron.
•Kidney stones — Published research linked long-term ketogenic use, especially in children with epilepsy, to a higher risk of renal stones.
•Bone health issues — Keto can reduce bone mineral density and increase markers of bone resorption, weakening bones over time.
•Thyroid dysfunction — Low carbohydrate intake may impair thyroid hormone conversion, leading to lower muscle mass.
Q: Does the ketogenic diet improve or worsen insulin resistance (HOMA-IR)?
A: Ketogenic diets initially improve insulin resistance, as shown by significant reductions in the HOMA-IR index (a measure of insulin sensitivity). This is mainly due to lowered carbohydrate intake, which decreases insulin demand and allows cells to regain responsiveness.
However, the improvements are not consistent across all individuals. In some studies, insulin sensitivity improved early but later plateaued or showed mixed results with extended ketosis. The variability depends on factors such as diet composition, physiological adaptation, and duration of adherence.
Q: What are the proven long-term effects of a ketogenic diet?
A: There are several long-term effects, many of which are still being studied:
•Weight loss plateaus — Initial fat loss typically slows or stops after six to 12 months.
•Altered lipid metabolism — Some people experience increased LDL cholesterol, as seen in case reports and trials, raising concerns about cardiovascular risk.
•Changes in gut microbiota — Long-term ketosis reduces microbial diversity and beneficial bacteria like Bifidobacterium, while increasing species such as Fusobacteria and Escherichia, both linked to colorectal cancer risk.
•Thyroid and hormonal adaptations — Extended carbohydrate restriction alters thyroid hormone levels and endocrine signaling.
Q: What are the overall effects of the keto diet on metabolic health?
A: Keto is a powerful short-term metabolic tool, especially for improving insulin resistance, Type 2 diabetes, and body weight regulation. It helps lower fasting glucose, improve HOMA-IR, and enhance early metabolic flexibility.
However, the overall long-term metabolic picture is complex. The same mechanisms that improve metabolism early — carbohydrate restriction and enhanced fat oxidation — can, over time, cause new physiological challenges. These include nutrient deficiencies, thyroid suppression, kidney strain, reduced bone density, and microbiome imbalances.
- 1, 2, 7 Sci Adv. 2025 Sep 19;11(38):eadx2752
- 3 Cleveland Clinic, Lipids
- 4, 5 Cureus. 2020 Jul 27;12(7):e9418
- 6 Nutrients. 2021 Mar 2;13(3):814
- 8 Cell. 2020 May 20;181(6):1263-1275.e16
- 9 Front Nutr. 2021 Jul 16;8:702802
- 10 Neuropediatrics. 2023 Oct;54(5):308-314
- 11 Front Endocrinol (Lausanne). 2020 Jan 21;10:880
- 12 PLoS One. 2022 Jun 3;17(6):e0269440
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