Objective To investigate the financial burden of in-patients with thyroid diseases in the West China Hospital in Chengdu, Sichuan province, from January 2011 to December 2012, 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: a) in 2011, 205 person-times were hospitalized in the department of endocrinology and metabolism, of which, 84 were male and 121 were female, with mean age of 45.3±15.7 years; b) for patients with thyroid diseases, median hospital stay was 10 days, the average cost of hospital stay for each patient was RMB 2 881.43 yuan, most of which was for lab tests and examination; c) the person-times of patients with hyperthyroidism was 162, accounting for 79.5% of the total of thyroid diseases, median hospital stay was 10 days, and the average cost of hospital stay was RMB 2 958.36 yuan; and d) there was no association between the number of hyperthyroidism complications and hospital stay and costs. Conclusion Thyroid diseases are a commonly-seen disease in the department of endocrinology and metabolism, of which, hyperthyroidism accounts for the most. There is no association between the number of hyperthyroidism complications and hospital stay/costs.