Background: Short-chain fatty acids (SCFAs) liberated by fermentation of complex carbohydrates might stimulate water and salt absorption, and provide energy. The aim of the study was to assess the number and proportion of faecal bacteria and the concentration of SCFAs of severely malnourished children with cholera receiving oral rehydration solution (ORS) containing glucose, amylase-resistant starch (ARS) or rice. Methods: Serial faecal samples were collected from 30 malnourished children with cholera until rehydration and partial nutritional recovery. SCFAs were identified and quantitated by high-performance liquid chromatography. In situ hybridization combined with flow cytometry was used to analyse the microbiota in the faeces. Results: Before treatment the concentration of total SCFA in faecal sample of cholera children was found to be 4.7±0.6 mmol/kg and it increased steadily until 95.0 ± 8.7 mmol/kg at day 28. Among different ORS groups, concentration was significantly higher in the Rice-ORS group at day 1 (Po0.011) and at day 2 (Po0.025). During recovery faecal output was significantly reduced and the number of bacteria also increased faster in the Rice-ORS group than in the glucose-ORS group at day 1 and day 2 (Po0.01), and a modest increase in bacterial number was observed in the glucose-ORS plus ARS group (day 1, P ¼ 0.07; day 2, P ¼ 0.09). Conclusion: Clinical recovery was associated with an increase in bacterial and SCFA concentrations with all three carbohydrates in ORS. However, the increases were significantly higher in children receiving Rice-ORS.