HIV-1-specific mucosal IgA antibodies may correlate with protection in highly exposed but uninfected individuals, but have been detected at highly variable levels in HIV-1-infected individuals. To determine the best assays for detection of IgA antibodies in mucosal samples, rectal washes from 16 HIV-1-infected and 14 uninfected individuals were distributed to six laboratories experienced in detection of mucosal antibodies. Assays for HIV-1-specific IgA and IgG were performed in a blinded fashion by each of the laboratories using modifications of ELISA and chemiluminescence-enhanced Western blotting. Rectal washes contained easily detectable total IgA levels that did not differ between HIV-1-infected and uninfected groups. Irrespective of the assay used, HIV-1-specific IgA antibodies were absent in most samples; only one laboratory identified a higher frequency of positive samples from HIV-1-infected than uninfected individuals. In spite of 10-fold lower levels of total IgG than IgA, all but one laboratory identified HIV-1-specific IgG in most rectal washes of HIV-1-infected individuals. Comparable and readily detectable levels of influenza-specific IgA antibodies were present in nasal, salivary, and rectal secretions from both HIV-1-infected and uninfected individuals. These observations suggest a selective alteration in the production of HIV-1-specific IgA antibodies in HIV-1-infected individuals.