The prevalence of chronic hepatitis B virus (HBV) infection in Denmark is not clear. The primary aim of this study was to estimate the prevalence of chronic HBV infection in Denmark. The capture–recapture method was used to estimate the total population diagnosed with chronic HBV infection in Denmark using four nationwide registers. The population with undiagnosed chronic HBV infection was estimated by incorporating data from a two-year nationwide HBsAg screening programme in pregnant women. We identified 4,466 individuals with chronic HBV infection in the four registers until the end of 2007, and the capture–recapture estimate of the total population diagnosed with chronic hepatitis B was 7,112 (95% confidence interval (CI): 6,953–10,747). Only 17% of the identified patients attended recommended clinical care according to national guidelines. Including undiagnosed patients, the current population alive with HBV infection was 10,668 (95% CI: 10,224–16,164), corresponding to a prevalence of 0.24% (95% CI: 0.23–0.37%) in the Danish population older than 15 years. The estimated prevalence of chronic HBV infection among adults in Denmark was lower than reported from other northern European countries. Only half of the infected population had been diagnosed, and a minority attended specialised clinical care.