Objective To investigate financial burden of in-patients with hypothalamus-pituitary-adrenal gland/gonad diseases in the West China Hospital of Sichuan University, 2011, so as to provide baseline data for further research. Methods The data of in-patients (who had been discharged from the department of endocrinology and metabolism or discharged after being transferred to other departments for diagnosis and treatment in the West China Hospital in 2011) were collected from the Hospital Information System (HIS) of the West China Hospital, including basic information, initial diagnosis when the patients were discharged, hospital costs, the information about whether the patients had been registered the insurance in hospital, etc. We classified diseases according to ICD-10 based on the initial diagnosis when the patients were discharged on the first page of case reports. The data were input using Excel 2010 software, and statistical analysis was performed using SPSS 13.0 software. Results The results showed that: in 2011, 352 person-times of in-patients with hypothalamus-pituitary-adrenal gland/gonad disease as first diagnosis were hospitalized in the department of endocrinology and metabolism, of which, 139 were male and 213 were female, with mean age of 42.9±15.0 years; and b) median hospital stay was 11 days, the average cost of hospital stay for each patient was RMB 4 361.09 yuan, most of which was for lab tests, examination, and biomedicine cost. Conclusion Hypothalamus-pituitary-adrenal gland/gonad diseases are an important health problem in the department of endocrinology and metabolism in a Triple-A Hospital. Most of hospitalization costs are for lab tests, examination, and biomedicine cost.