In this study, two different methodologies were compared for the detection of hepatitis B virus (HBV) DNA in the plasma of 28 patients and 36 controls. Method 1 was a nested polymerase chain reaction (PCR) followed by product detection in an ethidium bromide stained gel, whereas method II was a commercial single step PCR with digoxigenin labeled product captured by a probe and then detected in a digoxigenin-antidigoxigenin enzyme-linked immunosorbent assay (DIG ELISA). The results indicate that both methods are comparable showing a concordance of 98.4%, there was no statistically significant difference in the detection rates. We feel that any one of these assays may be suitable in a clinical laboratory setting, though the commercial assay may offer some advantages to laboratories without sufficient skilled staff in trouble-shooting PCR related problems.