We used a two-source capture-recapture method to estimate the number of patients diagnosed at the time of primary HIV infection in France between 1999 and 2002. The sources were the French PRIMO cohort and the French Hospital Database on HIV. The estimated number of patients was 325 per year, which represents only 5% (approximately 6000 cases) of all new cases diagnosed each year and only 8% of all new infections (approximately 4000 cases).