The humoral response to invading mucosal pathogens comprises multiple antibody isotypes, derived from systemic and mucosal compartments. To understand the contribution of each antibody isotype/source to the mucosal humoral response, parallel investigation of the specificities and functions of antibodies within and across isotypes and compartments is required. The role of IgA against HIV-1 is complex, with studies supporting a protective role as well as a role for serum IgA in blocking effector functions. Thus, we explored the fine specificity and function of IgA in both plasma and mucosal secretions important to infant HIV-1 infection: breast milk. IgA and IgG were isolated from milk and plasma from 20 HIV-1 infected lactating Malawian women. HIV-1 binding specificities, neutralization potency, inhibition of virus epithelial cell binding, and antibody-mediated phagocytosis were measured. Fine specificity mapping showed IgA and IgG responses to multiple HIV-1 Env epitopes, including conformational V1/V2 and linear V2, V3, and C5. Env IgA was heterogeneous between the milk and systemic compartments (Env IgA t = 0.00-0.63, p=0.0046-1.00). Furthermore, IgA and IgG appeared compartmentalized, as there was a lack of correlation between the specificities of Env specific IgA and IgG (in milk, t = -0.07-0.26, p=0.35-0.83). IgA and IgG also differed in function: while neutralization and phagocytosis were consistently mediated by milk and plasma IgG, they were rarely detected in IgA from both milk and plasma. Understanding the ontogeny of the divergent IgG and IgA antigen specificity repertoires, and their effects on antibody function, will inform vaccination approaches targeted toward mucosal pathogens. [ABSTRACT FROM AUTHOR]