Why AST and ALT Are Elevated in Hypothalamic Amenorrhea—And Why It’s Not Fatty Liver Disease
Before we dive in, we want to give credit to the author. This was written by Cat, a graduate of our Holistic HA Practitioner (HHAP) Certification Program. Cat brings a deep understanding of the root causes of HA and is passionate about supporting women on the path to recovery through education, empowerment, and holistic strategies.
Liver enzymes such as AST (aspartate aminotransferase) and ALT (alanine aminotransferase) are frequently measured in bloodwork to evaluate liver health. When elevated, they can suggest liver injury or damage—but in the context of hypothalamic amenorrhea (HA), mild elevations of these enzymes often reflect metabolic stress and physiological adaptations rather than liver disease.¹
What Are AST and ALT and Why Do They Matter?
AST is found in both liver and muscle tissue. It is often released into the bloodstream when the liver or muscles are under stress—commonly during intense physical activity.⁴ ALT, while present in small amounts in muscle, is primarily concentrated in liver cells and is considered a more specific marker of liver stress or damage, particularly when related to malnutrition.²
In HA, these enzymes may appear elevated, not due to liver damage or liver disease, but rather as a result of the body’s adaptive response to chronic energy deficiency, increased physical training, low fat stores, and associated hormonal suppression.³ Enzyme and Bile Insufficiency
Digestive enzymes and bile acids are essential for breaking down and absorbing nutrients. (9) During HA, low energy availability causes the hypothalamus to suppress nonessential processes to conserve fuel. (10,12) This can include signals to the pancreas, liver, and stomach, reducing enzyme output, bile release, and gastric acid secretion. (10) When you start eating more, your gut is suddenly faced with larger, more varied meals, but its secretory capacity and motility haven’t yet caught up. This mismatch can cause bloating, reflux, cramping, or gas. With consistent, balanced nutrition, pancreatic enzymes, bile production, and gastric secretions gradually return to normal—a process that strengthens with nourishment, much like retraining a dormant muscle.
Why AST and ALT May Be Elevated in HA
HA is often triggered by a chronic energy deficit—a state in which the body is not receiving enough calories to support basic metabolic functions. This may result from undereating and overexercising, psychological stress, or a combination of all three - which is often the case.
To conserve energy and protect the body, the hypothalamus downregulates reproductive hormones and slows metabolic processes. These adaptations—meant to protect vital functions—can also influence biochemical markers like liver enzymes.³
Exercise and Muscle Breakdown: AST Elevation
When energy availability is low and physical activity is high, the body may begin breaking down muscle tissue for fuel. Since muscle contains high concentrations of AST, as it is broken down AST is released into the bloodstream. This results in elevated AST levels and mild ALT elevations as a result of muscle strain.5 A study by Mallinson et al. (2014) found that female athletes (with or without HA) had higher AST than non-athletes and oligo-amenorrheic athletes (those with irregular menstrual cycles) had higher ALT than eumenorrheic athletes and non-athletes. The study concluded that lower body fat and higher athletic activity were predictors of AST elevation⁵ and that the length of time someone had suffered from amenorrhea correlated with the elevations in ALT. ⁵
These findings support the idea that AST reflects muscular stress, while ALT tracks more closely with hormonal and nutritional state.
Low Body Fat and Undernutrition: ALT Elevation
In HA, individuals often have low fat mass and are undernourished. This can put significant metabolic pressure on the liver. The liver is a metabolic hub and it works to break down stored glucose (glycogen) to provide energy. As glycogen stores are depleted as a result of low energy availability, the liver shifts to gluconeogenesis, producing glucose from amino acids (proteins) and glycerol (fats).⁶ The liver also increases fatty acid oxidation to compensate for energy deficits, which can generate oxidative stress if prolonged or excessive.⁷ The additional stress of gluconeogenesis can overwhelm the liver and may lead to mild liver cell injury, causing ALT to leak into the bloodstream. This is not liver damage in the pathological sense, but rather a reflection of metabolic overload. This same phenomenon is well documented in anorexia nervosa, where malnutrition contributes to mild ALT elevations.⁸
Refeeding and ALT Fluctuations
In extreme cases of chronic undernutrition, refeeding (resuming adequate caloric intake) can also temporarily raise ALT. This is because the liver, previously underactive, must adapt to processing an increased nutrient load. Temporary enzyme elevations are expected and usually resolve with continued recovery.⁸
Does This Mean You Have Fatty Liver Disease?
While AST and ALT are commonly used to screen for liver conditions such as non-alcoholic fatty liver disease (NAFLD), elevations in these enzymes in the context of hypothalamic amenorrhea (HA) usually do not indicate true liver disease. In HA, there is typically no fat accumulation in liver cells, and enzyme elevations tend to be mild and reversible with proper nutrition, reduced training, and hormonal recovery.5-8
Instead, these elevated liver enzymes reflect the body’s adaptive response to energy deficiency. Specifically, AST is often elevated due to muscle stress from intense or prolonged training while ALT may rise due to metabolic strain on the liver caused by chronic undernutrition. These changes are not necessarily signs of liver damage or disease, but rather a reflection of the body under stress. With adequate fuelling and recovery, enzyme levels often return to normal.
However, it is essential that healthcare providers interpret these labs in the context of HA physiology. Misinterpretation can lead to unnecessary tests, anxiety, or misdiagnosis. Ongoing monitoring and guidance from a clinician who understands HA is crucial for a safe and effective recovery.
Concerned about elevated liver enzymes during HA recovery?
If changes in AST and ALT on your bloodwork are causing confusion or concern, you’re not alone. Many women with hypothalamic amenorrhea are told their labs suggest liver problems, when in reality these changes often reflect energy deficiency, high training loads, and metabolic stress.
That’s why our 1:1 coaching and group coaching programs are designed to help you interpret your labs in the context of HA recovery, so you’re not left guessing or worrying about results that may actually be part of your body’s adaptive response. At The HA Society, we combine science-based education with individualized guidance to help you restore your cycle while supporting metabolic and hormonal health.
And if you're a practitioner, or want to become one, who wants to truly understand how lab markers like AST and ALT fit into HA physiology, our Holistic Hypothalamic Amenorrhea Practitioner (HHAP) Certification Program teaches you how to confidently interpret bloodwork and support clients through recovery using evidence-based, whole-person care.
Keep Reading
References:
Lala, V., Zubair, M., & Minter, D. A. (2023). Liver Function Tests. StatPearls. https://www.ncbi.nlm.nih.gov/books/NBK482489/
Moriles, K. E., Zubair, M., & Azer, S. A. (2024). Alanine Aminotransferase (ALT) Test. StatPearls. https://www.ncbi.nlm.nih.gov/books/NBK559278/
Roberts, R. E., Farahani, L., Webber, L., & Jayasena, C. (2020). Current understanding of hypothalamic amenorrhoea. Therapeutic Advances in Endocrinology and Metabolism, 11, 2042018820945854. https://doi.org/10.1177/2042018820945854
Pettersson, J., et al. (2008). Muscular exercise can cause highly pathological liver function tests in healthy men. British Journal of Clinical Pharmacology, 65(2), 253–259. https://doi.org/10.1111/j.1365-2125.2007.03001.x
Mallinson, R. J., et al. (2014). Body composition, hemodynamic, and biochemical parameters in young female normal-weight oligo-amenorrheic and eumenorrheic athletes and non-athletes. Journal of Clinical Endocrinology and Metabolism. PMC4268142
Murray, B., & Rosenbloom, C. (2018). Fundamentals of glycogen metabolism for coaches and athletes. Nutrition Reviews, 76(4), 243–259. https://doi.org/10.1093/nutrit/nuy001
Allameh, A., et al. (2023). Oxidative stress in liver pathophysiology and disease. Antioxidants, 12(9), 1653. https://doi.org/10.3390/antiox12091653
Mehler, P. S., & Brown, C. (2015). Anorexia nervosa: Medical complications. Journal of Eating Disorders, 3, 11. https://doi.org/10.1186/s40337-015-0040-8
