MUC2 and intestinal trefoil factor (ITF) are considered to have important roles in intestinal mucosal protection and epithelial repair. In order to investigate whether these genes are co-ordinately expressed, we have used competitive reverse transcription-polymerase chain reaction assays to measure MUC2 and ITF mRNA levels in human intestinal cell lines and along the longitudinal axis of rat intestine. ITF mRNA was expressed in several intestinal cell lines. However, MUC2 mRNA was detected only in LS174T cells where it was present at approx. 25-fold lower levels than the ITF transcript. In contrast, in rat intestinal tissues, MUC2 mRNA levels were generally higher than ITF mRNA levels. The levels of both transcripts increased markedly during postnatal development. In adult rats, the expression patterns of MUC2 and ITF mRNAs along the longitudinal axis of the small intestine were similar, with lowest levels in the proximal duodenum and relatively constant levels in the other regions assayed. In contrast, the expression patterns of MUC2 and ITF in different regions of the large intestine showed a marked divergence. Our results strongly suggest that expression of the MUC2 and ITF genes is not coordinately regulated in intestinal cells.