Background Humoral immune responses are often the hallmark of efficient vaccines. The recent RV144 vaccine trial has turned attention to the stimulation of humoral immune response as a potential mode of action for HIV vaccines. Therefore, detailed monitoring of antibody reactivities in patient specimens before and after vaccination is crucial. The determination of these reactivities on a sub-protein level provides information on the site of antigen/antibody interaction. In contrast to assays relying on whole antigens such as ELISA, peptide microarrays are efficient tools to deliver such information. Besides, complex peptide libraries can cover HIV sequence diversity, a special challenge provided by this virus.