BACKGROUND: Although lactulose and polyethylene glycol are osmotic laxatives widely used in the treatment of chronic constipation, no study has been conducted to compare their actions on the colonic bacterial ecosystem, which has an important influence on host health. AIM: To assess the effects of lactulose and polyethylene glycol on the composition and metabolic indices of the faecal flora in patients with chronic idiopathic constipation. METHODS: Sixty-five patients with chronic idiopathic constipation were included in this controlled, multi-centre, randomized, parallel-group study. Participants received lactulose (Duphalac) or polyethylene glycol-4000 (Forlax) powders for the first week at a fixed dosage at night (20 g/day); in the second week, patients were given the option to vary the dose according to efficacy and tolerance (10-30 g/day); for the last 2 weeks, treatment was administered at a fixed dosage based on the results of the second week (10-30 g/day). Stools were recovered for bacteriological analysis at days -1, 21 and 28. RESULTS: Clinical efficacy and tolerance were similar with both treatments. In the lactulose group, an increase in faecal bifidobacteria counts (P = 0.04) and beta-galactosidase activity (P < 0.001) was observed from day -1 to day 28, whereas, in the polyethylene glycol group, there was a decrease in total short-chain fatty acids (P = 0.02), butyrate (P = 0.04), acetate (P = 0.02) and faecal bacterial mass (P = 0.001). No differences were observed in stools with regard to the following parameters: counts of Lactobacillus, clostridial spores, Bacteroides and enterobacteria, pH, biliary acids and neutral sterol concentrations. CONCLUSIONS: Both lactulose and polyethylene glycol are efficacious and well tolerated. However, although lactulose can be considered as a pre-biotic in constipated patients, polyethylene glycol produces signs of decreased colonic fermentation in the stool.