BACKGROUND: There are few epidemiological data available on rare skin cancer, including Merkel cell carcinoma, Paget's disease, adnexal carcinoma, and sarcoma. We conducted this study to investigate the epidemiology of rare skin cancer diagnosed in the department of Doubs from 1980 to 2004. METHODS: Data were collected from a population-based cancer registry from 1980 to 2004. Diagnosis was based on the 3(rd) edition of the International Classification of Diseases for Oncology. The incidence rates were standardized on world population. RESULTS: One hundred and fifty one patients were investigated (88 women and 63 men). Median age for the diagnosed disease was 63 years. The standardized incidence rate was 0.82/100 000 person-year (95% CI = 0.68-0.96) and increased from 0.25 in 1980-1984 to 1.50 in 2000-2004. Fifty nine cases (39%) were sarcomas, 35 (23%) adnexal carcinomas, 27 (18%) Merkel cell carcinoma and 27 (18%) Paget's disease. The standardized incidence rates were 0.37/100 000 (0.27-0.47) for sarcomas, 0.16 (0.10-0.22) for adnexal tumors, 0.13 (0.08-0.18) for Merkel cell carcinoma, and 0.15 (0.09-0.21) for Paget's disease. CONCLUSIONS: Our results based on a population-based cancer registry showed an increase of the standardized incidence rate for all types of rare skin tumors. These results may be useful when considering the growing interest in rare diseases in identifying risk factors and planning scientific research programmes.