Antibodies are proteins generated by B cells as part of a humoral immune response, and play an important role in conferring immunological protection to infectious diseases through both natural exposure and vaccination. Advances in high-throughput technologies for examining antigen-specific antibodies made by single B cells, and in next-generation sequencing technologies, are making it possible to examine how the repertoires of B cells develop and change in response to infection or interventions like vaccines. In our lab, we apply technologies for single-cell analysis based on dense arrays of subnanoliter wells (nanowells) to characterize multiple aspects of antigen-specific B cells. Some of these data include phenotypic traits, the isotypes, specificities, and relative affinities of the antibodies, and the genes encoding the unique features of the antibodies. The nanowell-based platform makes it possible to perform the same analyses on B cells across a variety of anatomical compartments, regardless of the numbers of cells available, including mucosal tissues, bone marrow, and peripheral blood. These techniques are suitable for evaluating B cells, or transformed cells such as hybridomas, from a range of hosts, including human, non-human primates, and mice. Combining these comprehensive profiles of antigen-specific responses for antibody-secreting cells (or activated B cells) with broader measures of the B cell repertoire enabled by new advances in next-generation sequencing is enabling an in-depth characterization of antibody repertoires in diseases such as HIV, West Nile Virus, and food allergies, as well as those generated following vaccination. Such insights may inform how the humoral response emerges in infection and may yield unique antibodies with potential therapeutic or diagnostic uses.