The small intestinal epithelium plays an important role in the mucosal host defense. Intestinal epithelial cells have been known to release substances that suppress lymphocyte proliferation, suggesting an immunoregulatory function. We investigated how intestinal epithelial cells affect lymphocyte proliferation. Serum-free medium that was conditioned by incubating epithelial cells, particularly crypt cells, of the rat small intestine affected proliferation of allogeneic spleen lymphocytes stimulated with concanavalin A, as assessed by measuring cellular [3H]thymidine incorporation. Less than 1% and greater than 2% of the conditioned medium enhanced and suppressed, respectively, lymphocyte proliferation. The causative substances found in the conditioned medium were dialyzable and heat-stable. Suppression was not due to toxicity to splenocytes. Exposure of splenocytes to a suppressive concentration of the conditioned medium beginning at 30 min before an onset of lectin stimulation decreased the suppression of lymphocyte proliferation. Splenocyte exposure to the suppressive concentration of the conditioned medium beginning at 30 min to 4 h after the onset of the stimulation inversely strengthened the suppression. A brief exposure of splenocytes to the conditioned medium for the last 4 h during a total 72-h culture period still suppressed lymphocyte proliferation. Thus, intestinal epithelial cells produce low-molecular-weight lymphocyte proliferation-modulating substances that suppress the proliferation of lectin-activated lymphocytes, but not resting ones, by affecting earlier intracellular events and the following DNA synthesis when incubated in culture medium.