BackgroundHepatitis B is a major health concern in Africa. The vaccine against hepatitis B virus (HBV) was introduced into the Expanded Programme on Immunization (EPI) of Cameroon and Senegal in 2005, and of CAR (Central African Republic) in 2008. A cross-sectional study was conducted to assess HBV immunization coverage following the vaccine’s introduction into the EPI and factors associated with having been vaccinated.MethodsAll hospitalized children, regardless of the reasons for their hospitalization, between 3 months and 6 years of age, for whom a blood test was scheduled during their stay and whose condition allowed for an additional 2 mL blood sample to be taken, and who provided the parent’s written consent were included. All children anti-HBs- and anti-HBc + were tested for HBsAg.Vaccination coverage was assessed in three different ways: immunization card, maternal recall and serologic anti-HBs profile.Results1783 children were enrolled between April 2009 and May 2010. An immunization card was only available for 24 % of the children. The median age was 21 months.Overall HBV immunization coverage based on immunization cards was 99 %, 49 % and 100 % in Cameroon, CAR and Senegal, respectively (p < 0,001). The immunization rate based on maternal recall was 91 %, 17 % and 88 % in Cameroon, CAR and Senegal, respectively (p < 0,001). According to serology (anti-HBs titer ≥ 10 mUI/mL and anti-HBc-), the coverage rate was 68 %, 13 % and 46 % in Cameroon, CAR and Senegal, respectively (p < 0,001). In Senegal and Cameroon, factors associated with having been vaccinated were: mother’s higher education (OR = 2.2; 95 % CI [1.5–3.2]), no malnutrition (OR = 1.6; 95 % CI [1.1–2.2]), access to flushing toilets (OR = 1.6; 95 % CI [1.1–2.3]), and < 24 months old (OR = 2.1; 95 % CI [1.3–3.4] between 12 and 23 months and OR = 2.7; 95 % CI [1.6–4.4] < 12 months). The prevalence of HBV-infected children (HBsAg+) were 0.7 %, 5.1 %, and 0.2 % in Cameroon, CAR and Senegal, respectively (p < 0.001).ConclusionsAssessing immunization coverage based on immunization cards, maternal recall or administrative data could be usefully reinforced by epidemiological data combined with immunological profiles. Serology-based studies should be implemented regularly in African countries, as recommended by the WHO. Malnutrition, lack of maternal education and poverty are factors associated with vaccine non-compliance. The countries’ vaccination programs should actively address these problems.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-1000-2) contains supplementary material, which is available to authorized users.