In comparison with other Canadian provinces and most Western countries, the province of Manitoba maintains a different vaccination policy for hepatitis B. This policy provides selective antenatal screening for hepatitis B in women and an inoculation program for hepatitis B vaccination for fourth-grade pupils. There has been increasing concern for this policy with regard to its influence on secular trends of acute hepatitis B incidence in Manitoba. This created a need to summarise the epidemiological characteristics of hepatitis B virus (HBV) infection in Manitoba and to allocate finances and human resources for future prevention programs. The Cadham Provincial Laboratory in Winnipeg, a Canadian Public Health Laboratory, is responsible for testing all specimens for diagnosis of various common infectious diseases in Manitoba. During the period from 1 January 1992 to 31 December 2003, a total of 285,946 clinical specimens were submitted to this laboratory, which confirmed 310 cases of acute HBV and 7,556 cases of chronic HBV infection. A total of 18,168 individuals were identified as having vaccine-induced immune status. The incidence rate of acute HBV infection has significantly decreased from 6.52/100,000 person-years in 1996 to 0.86/100,000 person-years in 2003. Annual prevalence rates of chronic HBV infection in Manitoba increased slightly from 42.96 cases/100,000 population in 1992 to 71.47 cases/100,000 population in 2003. Incidence rates were generally higher in men than in women at all age groups, with values of 2.65 and 1.65 per 100,000 population, respectively (chi-square=15.768, p value <0.001). The highest incidence rate for both males and females was observed in the age group 30-34 years. The North Eastman and Winnipeg Regional Health Authorities showed significantly higher incidence rates of acute hepatitis B compared with the other nine Regional Health Authorities. Selective hepatitis B vaccination programs for children in Manitoba had achieved the greatest success in the prevention of vertical and horizontal transmission. There is an urgent need to develop cost-effective harm-reduction strategies for hepatitis B prevention among adults (aged 30-34) and groups at risk in Manitoba.