Although intraepithelial T lymphocytes of the large intestine (LI) are known to differ from those of the small intestine (SI) in phenotype and function, differences in LI and SI lamina propria (LP) lymphocyte populations have not been clearly established. In this work we found striking phenotypic differences between SI and LI LP lymphocyte populations from Balb/c mice analyzed by flow cytometry. In the LI most lymphocytes were B cells and the predominant T cells were TCR-alpha beta+, CD8+. In contrast, in the SI most T lymphocytes were CD4+ expressing TCR-alpha beta+, although a higher proportion expressed TCR-gamma delta+ than in the LI. In T cells the expression of adhesion molecules and cytokines was also different between SI and LI. The proportion of LP T cells expressing alpha4beta7 and L-selectin was higher in the LI than in the SI; whereas a greater proportion of cells expressing alpha(E)beta7 were detected in the SI than in LI. Higher proportions of T cells expressing L-selectin and alpha4beta1 were detected in the intraepithelial compartment of the LI than that of the SI, whereas the number of T cells expressing alpha(E)beta7 was much higher in the SI than in the LI. The proportion of T cells spontaneously producing IL-2, IFN gamma, and IL-4 at the intraepithelial and lamina propria, in the small and large intestine, was different indicating that distinctive functional features exist in the lymphocyte populations residing at the different intestinal compartments.