The effect of regular consumption of the low-digestible and prebiotic isomalt versus the digestible sucrose on gene expression in rectal mucosa was examined in a randomized double-blind crossover trial. Nineteen healthy volunteers received 30 g isomalt per day or 30 g sucrose as part of a controlled diet over two 4-week test periods with a 4-week washout period in between. At the end of each test phase rectal biopsies were obtained. After RNA extraction mucosal gene expression was assayed using GeneChip microarrays. In addition, expression of cathelicidin hCap18/LL37, cellular detoxification enzymes GSTpi, UGT1A1 and CYP3A4, cyclooxygenase 2 and barrier factors MUC2 and ZO-1 were determined by real-time RT-PCR. Microbiological analyses of fecal samples revealed a shift of the gut flora towards an increase of bifidobacteria following consumption of the diet containing isomalt. Isomalt consumption did not affect rectal mucosal gene expression in microarray analyses as compared to sucrose. In addition, the expression of cathelicidin LL37, GSTpi, UGT1A1, CYP3A4, COX-2, MUC2 and ZO-1 was not changed in rectal biopsies. We conclude that gene expression of the human rectal mucosa can reliably be measured in biopsy material taken at endoscopy. Dietary intervention with the low digestible isomalt compared with the digestible sucrose did not affect gene expression in the lining rectal mucosa.