Regional variations in intraepithelial lymphocytes (IELs) in the small intestine were examined in alymphoplasia mutant (aly/aly) mice, which are characterized by the systemic absence of lymph nodes and Peyer's patches, and heterozygous (aly/+) mice. The small intestines were taken from 10 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 a flow cytometer. The number of IELs in the distal part was significantly fewer in aly/aly mice compared with aly/+ mice, although the total number of small intestinal IELs were comparable between them. As to the IELs subsets, regional variations in alphabeta T cells and gammadelta T cells were observed in aly/+ mice, but they disappeared in aly/aly mice. However, regional variations in composition of alphabeta T cell subsets were similarly observed in both aly/aly mice and aly/+ mice. This indicates that, although not essential, mesenteric lymph nodes (MLN) and/or Peyer's patches may modify the regional variations in IELs.