The cause of thymoma is unknown. No population-based study has described demographic patterns of thymoma incidence. Previous reports have linked thymoma with diverse subsequent malignancies, but these associations are uncertain. We used Surveillance, Epidemiology and End Results (SEER) data to study the incidence of malignant thymoma by sex, age and race in the United States (1973–1998). Incidence was modeled with joinpoint regression (for age) and Poisson regression. We also used SEER data to compare malignancies following thymoma diagnosis with those expected from general population rates, calculating the standardized incidence ratio (SIR, observed/expected cases) to measure risk. The overall incidence of malignant thymoma was 0.15 per 100,000 person-years (849 cases). Thymoma incidence increased into the 8th decade of age and then decreased. Incidence was higher in males than females (p=0.007) and was highest among Asians/Pacific Islanders (0.49 per 100,000 person-years). Following thymoma, there were 66 malignancies (SIR 1.5, 95%CI 1.2–1.9). The most notable excess risk for subsequent malignancy was for non-Hodgkin's lymphoma (B immunophenotype) where the SIR was 4.7 (95%CI 1.9–9.6, 7 cases). There were also excess digestive system cancers (SIR 1.8, 95%CI 1.1–2.9) and soft tissue sarcomas (SIR 11.1, 1.3–40.1). No other cancers were increased after thymoma. In conclusion, malignant thymoma is extremely rare. The peak in late adulthood deserves further study. Variation in incidence by race suggests a role for genetic factors. Our study did not demonstrate broadly increased risk for malignancies following thymoma. © 2003 Wiley-Liss, Inc.