This study used flow cytometry to identify graft cells in the recipient peripheral blood and spleen and host cells infiltrating the graft mesenteric lymph node and Peyer's patches after heterotopic rat small bowel transplantation. Transplantation had little effect on the overall cell subset composition of these compartments and no changes appeared characteristic or indicative of developing rejection, suggesting that physiological control of cell migration remained unaltered. A small and transient population of graft cells was detected in the peripheral blood and spleen of the recipient which disappeared after 5 and 3 days respectively. Graft-derived cells in the peripheral blood comprised predominantly CD4+ cells on day 1 with B cells predominating on day 5. Graft cells infiltrating the spleen were predominantly B cells. Host cells infiltrated the graft mesenteric lymph nodes and Peyer's patches to a lesser extent than previously reported using immunohistochemical analysis. For both tissues, infiltrating host-derived cells initially comprised mainly CD4+ cells. On day 4 approximately equal proportions of CD4+ and B cells were present in the mesenteric lymph node, whereas B cells were predominant in the host cell infiltrate of the graft Peyer's patches. In summary, these findings indicate that the cell subset composition of recipient and graft lymphoid compartments does not change after small bowel transplantation, even in the presence of a substantial recipient cell infiltration. The reasons for the apparent discrepancies in the degree of host cell infiltration when assessed using immunohistochemical and flow cytometric techniques are currently uncertain, but may result from the localised release of soluble MHC class I in graft tissues as a consequence of infiltrating host cell activation or localised cell destruction.