BACKGROUND: Cystic fibrosis (CF) patients grow poorly and tend to be malnourished. They frequently suffer from lung infections necessitating the repeated use of antibiotics. AIM: This study was conducted to determine whether supplementation with a probiotic Lactobacillus reuteri (L. reuteri) could reduce the incidence and duration of lung infections, and whether this would impact on their anthropometric data. The secondary purpose was to compare the nutritional status of the CF patients attending CF clinics in Kwazulu-Natal (KZN) with CF patients attending CF clinics in Cape Town (CT). METHODS: Twenty three CF patients 6-31 years of age from 2 CF clinics in Kwazulu-Natal started the study although only 16 patients completed it. The study was a randomized, double blind, placebo controlled crossover trial with six months on placebo and six months on probiotic. Weight, height, mid arm circumference (MAC), triceps skin fold thickness (TSF), forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) were measured, sputum collected and a symptom diary completed over the 12 month period. Anthropometric data of CF patients attending CF clinics in CT was obtained from the publication by Westwood & Saitowitz (1999). RESULTS: Compliance with taking the L. reuteri was poor. Most took only 50% of the required daily dose. Probiotic supplementation showed a slight (non significant) trend to improve FEV1 and FVC, while no significant difference could be seen in the number and duration of the lung infections. Sputum analysis showed a non significant trend towards the probiotic reducing the number of bacteria in the sputum. There was a significant reduction of symptoms for fever, running nose, sore throat and ear ache while on placebo. There was a significant increase in weight gained off probiotic compared to the probiotic period. The changes in height, weight for age (WFA) percentiles, height for age (HFA) percentiles, WFA and HFA Z-scores, percentage expected weight for age and percentage expected height for age all showed no difference whether on or off probiotic. Over half the CF children in the KZN clinics were underweight for their actual height compared to one third in the CT clinics with a higher number of subjects below the 5th percentile for MAC and TSF readings compared to CT. CONCLUSION: Due to a small sample size and poor compliance no firm conclusions could be drawn. However a slight (non significant) improvement could be seen in favour of the probiotic for FEV1, FVC, and sputum analysis. Although all other findings were not significantly different it would be of benefit to carry out further investigation with improved compliance with the probiotic to see if the parameters set out above could be improved. The KZN and CT CF groups were comparable and the nutritional status of CF patients on KZN was well below that of the CT CF clinics and further monitoring would need to be carried out.