We audited adherence to national hepatitis B virus (HBV) immunisation policy for neonates and infants born to HBV positive mothers in two counties of England during 2007/08 to 2011/12 (n=112 in County X, n=190 in County Y). Over the five year period, 29.9% of at risk neonates in County X and 23.5% in County Y required hepatitis B immunoglobulin (HBIG) at birth. The annual median age of HBIG administration was 0.0–0.5 days. The annual median coverage and timeliness of the first (coverage range 92.3–100.0%; age of administration range 0.0–0.0 days), second (83.8–100.0%; 32.0–42.0 days), third (81.1–100.0%; 62.0–81.0 days) and fourth dose HBV immunisations (44.4–91.9%; 378.0–443.0 days) and serological testing (8.6–81.0%; 450.0–707.0 days) were calculated. Statistically significant variation was found in the coverage of third and fourth dose immunisations in County Y, age of fourth dose immunisation in County X, and the coverage and timeliness of serological testing in both counties (p < 0.05). HBIG and the first three HBV immunisations were commonly administered according to the national schedule. Fourth dose immunisations and serological tests showed poor adherence. We advocate public health interventions to improve immunisation programme outcomes and hepatitis B surface antigen testing.