Background Transaldolase (TALDO) deficiency (OMIM #606003) is a rare autosomal recessive multi-systemic disorder of carbohydrate metabolism. It has a vast phenotypic spectrum ranging from neonatal liver failure to slowly progressive liver cirrhosis and is characterized by intrauterine growth restriction, hepatosplenomegaly, bicytopenia, nephrolithiasis, and congenital heart disease. Methods and results We report a patient with a late-onset form of TALDO deficiency characterized by hypergonadotropic hypogonadism and slightly elevated levels of alpha-fetoprotein (AFP). A novel TALDO1 mutation was detected through the application of reverse genetics with the use of clinical exome sequencing (CES). Conclusion This report provides further evidence that reverse genetics is a useful approach in patients who do not manifest the hallmark features of known and recognizable syndromes. TALDO deficiency should be considered in the differential diagnosis of unexplained elevated AFP levels and hypergonadotropic hypogonadism with microlithiasis.