The isolation of intestinal intraepithelial lymphocytes (IEL) is a major prerequisite for the investigation of cellular and molecular cross-talk in the intestinal mucosa. Since intestinal epithelial cells exhibit distinct functional features at the villi tip and crypt levels, such differences could extend to IEL. We developed a mechanical procedure for isolation of IEL from these distinct epithelial sites to test our hypothesis. Cells isolated from the intestinal epithelium by sequential incubations under stirring were segregated based upon their alkaline phosphatase (AP) activity since villi tip and crypt fractions expressed high and low AP activity, respectively. IEL preparations obtained after a further purification step in Percoll gradient contained >90% Integrin α(IEL) chain+, CD3+ T cells, and no Ig+ cells. Villi tip IEL preparations possessed increased numbers of low density IEL when compared to crypt IEL, suggesting that distinct IEL-epithelial cell interactions occur at the intestinal villi tip and crypt levels.