Upper jejunum and terminal ileum were examined in specified-pathogen-free (SPF), conventional and conventional after SPF rearing (ex-SPF) rats. The effect of 2 different diets on the last 2 groups was examined. Ex-SPF rats had taller villi and deeper crypts than SPF rats, but similar crypt to villus ratios and cell production rates. Ex-SPF rats had similar crypt depth and jejunal villus height to conventional rats on the same diet, but taller ileal villi and a lower cell production rate. Even after 6-8 weeks in a conventional environment, ex-SPF rat intestine was still not identical with conventional rat intestine. Diet had a significant effect on mucosal architecture, and a smaller effect on cell production rate. It is concluded that diet, microbiological status of colony of origin, and environment after weaning, can all affect mucosal architecture and epithelial cell production, and should be properly controlled in experimental studies.