For the past decade, a specific hepatitis B virus (HBV) genotype A strain has been prevalent among men having sex with men (MSM) in Amsterdam, the Netherlands. At what point in time this strain was introduced in the MSM population, and why only this specific strain continues to be transmitted, remains unclear. Between 1984 and 2003, sera of 1862 MSM were retrospectively screened for anti-HBc in the context of the Amsterdam Cohort studies. After 2003, most MSM participating in this study were vaccinated, making further testing less useful. HBV DNA from anti-HBc seroconverters was amplified and sequenced. Poisson regression was used to test for temporal trends in HBV and HIV incidence. Of the 1042 MSM who were negative for anti-HBc at entry, 64 had seroconverted during follow-up at a median age of 32. At the point of seroconversion, 31 MSM were HIV positive. HBV incidence declined dramatically in the first years and then remained stable throughout the study period. The HBV and HIV incidence ran almost in parallel. With the exception of three MSM, all were infected with genotype A. Fifteen of these (41%) were infected with an identical genotype A strain. For the past two decades, an identical genotype A strain has been circulating among MSM in the Netherlands. Although HBV is generally considered more infectious than HIV, this study shows that the trend and magnitude in HBV and HIV incidence among MSM are similar.