Mucosal tissues of the gastrointestinal and genitourinary tracts serve as major portals of HIV-1 transmission, and recent literature has highlighted the important role of these tissues in pathogenesis. However, our understanding of human mucosal T-cell responses remains limited. We have previously reported methods for isolating, culturing and analyzing mucosal T-lymphocytes obtained from gastrointestinal biopsy tissue. This method of acquiring tissue is minimally invasive and well accepted by patients, and allows sampling of sites that would not otherwise be accessible without surgical intervention. This chapter summarizes the approach currently in use in our laboratory to isolate and study and T-cells from rectal biopsies obtained through flexible sigmoidoscopy. These methods are also applicable, with minor modifications, to small tissue samples obtained from other lymphoid tissues.