Abstract : Hepatitis B virus (HBV) infection remains a major global health concern particularly in developing countries. Accurate diagnosis is essential for early treatment and prevention of transmission. To compare serological detection of hepatitis B surface antigen (HBsAg) with molecular detection of HBV DNA using real time polymerase chain reaction(rt-PCR). A hospital-based cross-sectional study was conducted on 66 patients over one year. Serum samples were tested for HBsAg using a rapid immunochromatographic assay and for HBV DNA using rt-PCR. Diagnostic performance parameters were calculated. HBV DNA was detected in 4(6.1%) patients by rt-PCR while HBsAg was positive in 2(3.03%) patients. Two cases showed discordant results suggestive of occult hepatitis B infection. Rt-PCR demonstrated a sensitivity of 66.7% and specificity of 100% when compared with serology. Real-time PCR detects additional HBV infections missed by serological testing and may be useful in identifying occult hepatitis B infections. However larger studies are required to validate diagnostic accuracy.