Gut development is stimulated by exposure to microorganisms, especially early-life microbial exposure. This study aimed to investigate whether doe-litter separation, which is performed in many rabbit farms, affects this exposure and therefore inhibits the development of intestinal system in suckling rabbits. Immediately after parturition, Rex rabbit does (n=16) were adjusted to 8 kits per litter and divided into doe-litter separation (DLS) group and doe-litter together (DLT) group based on the conditions of the does. One healthy kit per litter was selected and sacrificed at 7 d, 14 d, 21 d and 28 d of age, and the number of total bacteria, Escherichia coli and Bacteroides-Prevotella, expression of interleukin 6 (IL-6) and interleukin 10 (IL-10) in duodenum and caecum were investigated by real-time polymerase chain reaction. The morphological parameters of duodenum and vermiform appendix were also measured. Our results showed that doe-litter separation affected the number of intestinal bacteria. At 7 d of age, except for caecal Escherichia coli, the number of the investigated bacteria was decreased by doe-litter separation (P<0.05). But 1 wk later, only the number of total bacteria and Bacteroides-Prevotella in caecal content (P<0.05) and Escherichia coli in duodenal content from DLS kits (P<0.05) were still lower than those from DLT kits. After being provided with supplementary food for 7 d, DLS kits had fewer total bacteria in caecal content (P<0.05) and fewer E. coli in duodenal content (P<0.01) than DLT kits. After growing to 28 d of age, kits in DLS group still tended to have fewer total bacteria in caecal content, and expression of IL-10 and secretion of secretory IgA (sIgA) in vermiform appendix in DLS group was obviously lower than kits in DLT group (P<0.05). The villus height:crypt depth ratio in duodenum at 3 rd wk and 4 th wk was decreased by DLS (P<0.05). Kits in DLS group had shorter villus height (P<0.05), higher crypt depth (P<0.05) and shorter vermiform appendix (P<0.05) at the end of the trial. Furthermore, separating kits from the doe had a negative effect on their average daily gain at 3 rd wk and 4 th wk (P<0.05). Limiting the microbiological contact with the mother during suckling period affected the kits' intestinal flora and could negatively affect the development of intestinal digestive and immune system and growth performance of kits.