Background/Aims: Physical training is a well-known inducer of positive physiological adaptations. The effects of moderate physical training on the morphometry of splenic lymphoid follicles of endotoxemic rats submitted to a perinatal low-protein (LP) diet were evaluated. Methods: Male Wistar rats were divided into two groups according to their mother’s diet (17% casein, control, C) and, undernourished (8% casein, LP diet). On postnatal day 63, the animals were submitted to moderate physical training (8 weeks, 5 days·week^–1, 60 min·day^–1, at 70% of VO_2max). After the physical training period, half of each group received an injection of either lipopolysaccharide (LPS) or saline. Plasma corticosterone concentration, blood differential leukocyte counts and splenic morphometric parameters were analyzed. Results: In undernourished toxemic (LP + LPS), LPS increased plasma corticosterone concentrations, but not in previously trained (LP + T + LPS) animals. Neutrophilia and lymphopenia in response to LPS was more pronounced in pups from undernourished mothers (LP + LPS). LP + LPS animals showed a higher increment (47.4%) in the number of lymphoid follicles, a reduction in the number and size of the splenic follicles, and in the marginal zone area. Those alterations were attenuated in trained animals (LP + T + LPS). Conclusions: Physical training attenuates the effects of nutritional programming on the splenic microanatomy by a mechanism that involves the hypothalamic-pituitary-adrenal axis.