The effect of Methoxychlor (MXC) on the thymus was examined in rat pups that were delivered from dams receiving MXC at a dietary concentration of 0 or 1500 ppm for a period from pregnancy to lactation. The pups of both sexes were euthanized on postnatal days (PNDs) 7, 14, and 21. Histologically, the thymus showed marked depletion of cortical lymphocytes on PND 7 and also had an increase in lymphophagocytosis in the cortical area on PNDs 14 and 21. Morphometrical analysis disclosed that both cortex and medulla of the thymus from treated pups were reduced in size, but the reduction was more evident in the cortex. A significant increase in transferase-mediated dUTP nick end labeling-positive cells was detected in the cortex area, corresponding to the presence of lymphophagocytosis. Flow cytometric analysis revealed a significant decrease in the double positive (CD3(int)CD4(+)CD8(+)) immature cells on PND 21. These results have suggested that MXC may impair maturation of thymic lymphocytes in rat pups, which results in enhancement of apoptosis leading to thymic atrophy during the postnatal period.