The regional variation in the intraepithelial lymphocytes (IELs) in the small intestine was examined in BALB/c male and female mice and C3H/He and C57BL/6 male mice. The small intestines were taken from 11 to 12-week-old mice and divided equally into 3 parts (the proximal, middle and distal parts). IELs were isolated from each part of the intestine and analyzed with flow cytometer. The number of IELs was highest in the proximal part and lowest in the distal part. The distribution of IEL subsets was markedly different between the proximal and the distal parts, and that in the middle part showed the intermediate pattern. The percentage of alphabeta T cells were higher in the distal part. In alphabeta T cell subset, the percentage of CD8alphaalpha T cells was higher in the proximal part, whereas those of CD4 and CD4CD8alphaalpha double positive T cells were higher in the distal part. In gammadelta T cell subset, no regional variations were found. The regional variations in the number and subsets of IELs showed almost the same patterns between male and female BALB/c mice and similar patterns among three strains of mice. This strongly suggests that the regional variations in the small intestinal IELs are common to mouse species.