Introduction: Identification of hepatitis B virus carriers in blood donors is imperative in order to avoid transmission of the disease via blood transfusion. Objective: To determine if blood donors with positive results for serological markers HBsAg and anti-HBc were hepatitis B virus DNA carriers. Methods: 12,745 samples were collected from six Ecuadorian blood banks and analyzed for HBsAg, anti-HBc and anti-HBs infectious markers by automated ELISA. All samples that tested positive for one, two or all three markers were analyzed with molecular techniques to determine the presence of viral DNA. Results: 27.5 % of the samples that were reactive for anti-HBc alone and 100 % of those with positive results for HbsAg and IgM/IgG anti-HBc were identified to contain hepatitis B virus DNA (p = 0.001). Conclusions: The selection of infection markers, as well as the detection methods define the results. Performing two serological and one molecular test is important in order to identify hepatitis B virus carriers and prevent its transmission.