The aim of this study was to investigate the influence of apoptosis on Peyer's patches and the intestinal immunoglobulin A (IgA) response in burned mice. Sixty male Balb/c mice were randomly assigned into the sham-burn (control) group (n=30) and the burn group (n=30). The mice in the burn group received a full-thickness scald burn over 20% of the total body surface area (TBSA), on the back. At 12, 24 and 72 h, respectively, after injury, the burned mice (n=10, at every time point) were anaesthetised and their entire intestines were collected. The mice in the sham-burn group were treated with the same procedure as above, except for the burn injury. The number of Peyer's patches on every entire intestine and the total Peyer's patches cell yield were counted. The changes of lymphocyte subpopulations in Peyer's patches were measured by flow cytometry (FCM). And the levels of intestinal IgA were examined by enzyme-linked immunosorbent assay (ELISA). Fluoresceinisothiocyanate (FITC)-conjugated Annexin-tau and propidium iodide (PI) double-staining cells were analysed by FCM for apoptotic ratio in Peyer's patches. The results showed that the total Peyer's patch cell yield and the numbers of CD3, CD4, CD8 and CD19 cells were significantly decreased at 12, 24 and 72 h after injury (P<0.05), and that the intestinal IgA levels were markedly reduced at 24 and 72 h (P<0.05). On the other hand, total apoptotic ratio and all cell subpopulation apoptosis in Peyer's patches were dramatically increased at 12, 24 and 72 h after injury (P<0.05). These results indicated that severe burns led to a significant decrease in the number of Peyer's patch cells and in intestinal IgA levels, which was closely associated with strongly increased apoptosis in Peyer's patches.