Gender medicine (GM) deals with the effects of sex and gender differences between males and females. Since 2007, Tokyo Women's Medical University has operated the nation's largest Women-Specific Clinic based on GM, at which 13 female specialists in various fields collaborate. We perform differential diagnoses of complaints while considering gender and sex differences in the mind and in diseases, life stage, and social background. We analyzed the clinical data of 285 patients who visited us during the first year, 68% (195/285) of whom presented with undefined complaints that included menopausal symptoms, and 26.7% (52/195) of whom were found to have organ diseases which explained the undefined complaints after our differential diagnosis. Forty-three of 195 women had endocrine diseases and 29 of them had thyroid dysfunctions; the most frequent endocrine disease. In other words, the frequency of endocrine diseases among patients who were considered to have undefined complaints were 22% and the corresponding frequency of thyroid dysfunction was 15%. In particular, thyroid dysfunction symptoms overlapped with menopausal symptoms and were difficult to distinguish without thyroid function tests. However, the endocrine test is not included in the general test, which increased the difficulty in detecting endocrine diseases. We need to be aware that women generally have a higher incidence of endocrine disease than men and that some endocrine diseases occur during pregnancy, postpartum, or around menopause. Incorporating GM aspects into daily practices can improve the accuracy of the diagnosis overall, especially the diagnosis of endocrine diseases in women.