The mucosal immune systems of the genital and intestinal tracts are considered as the most frequent sites of HIV-1 entry, displaying remarkable immunological differences in the systemic immune compartment which must be considered in the evaluation of humoral and cellular immune responses to HIV- 1. Marked differences in the fluids from the genital and intestinal tracts and in plasma with respect to the Ig isotypes, their levels, molecular forms and distinct effector functions must be taken into consideration in the evaluation and interpretation of humoral immune responses. Because of the low levels and highly pronounced variation in Ig content, HIV-1-specific antibody concentrations should always be related to the levels of total Ig of a given isotype. This practice will avoid inevitable differences due to the small volumes of collected fluids and sample dilution during the collection and processing of samples from external secretions. Furthermore, appropriate controls and immunochemical assays should be used to complement and confirm results generated by ELISA, which is prone to false positivity. In the evaluation of antibodymediated virus neutralization in external secretions, precautions and rigorous controls must be used to exclude the effect of innate humoral factors. The evaluation of cell-mediated immune responses in mucosal tissues is difficult due to the low yields of cells obtained from tissue biopsies or cytobrush scrapings. Furthermore, tissue biopsies of, for example, rectal mucosa, provide information pertaining exclusively to this local site, which due to the differences in the distribution of cells of different phenotypes, does not provide generalized information to the entire intestinal tract. Importantly, studies concerning the kinetics of cellular responses are difficult to perform due to the limited availability of samples or the inability of obtaining frequently repeated tissue biopsies. For sampling the female genital tract, parallel collection of menstrual and peripheral blood yields high numbers of cells that permit their detailed phenotypic and functional analyses. In contrast to tissue biopsies, this non-traumatic collection procedure results in high cell yields and repeated monthly sampling permits extensive and parallel functional studies of kinetics and unique characteristics of HIV-1-specific cellular responses in the female genital tract and peripheral blood.