Malnutrition affects virtually all organ systems, and malnourished children are more prone to infections. These children have dysbiosis, but probiotics can restore the disrupted gut microbiome. We investigated the protective effects of Lactobacillus rhamnosus GG in malnourished children in terms of incidence of infection, and anthropometric and metabolic parameters. 50 intervention and 50 control patients, aged 6 months to 5 years, with body weight and height below -2 SD, were randomly and prospectively recruited. The controls received a calorie and protein-appropriate diet for 3 months, while the study group additionally received approximately 109 L. rhamnosus GG for 3 months. Infection episodes and nutritional status were compared between the groups. 38 intervention, 33 control patients completed the study and the two groups were similar at baseline. The study group had fewer upper respiratory tract infections and gastroenteritis episodes at each month and at the end of the study. Children in the study group experienced fewer total upper respiratory infections and urinary tract infections. Hospitalisation was more frequent in the control group during the third month and at the end of the study. Total infection numbers were higher in the control group at each month and at the end of the study (P<0.001 for each). Increments in body mass index (BMI) and BMI Z-scores were more pronounced in the study group (P=0.008 and P=0.02, respectively). Daily prophylactic use of L. rhamnosus GG at 109 bacteria in malnourished children prevents most infections and improves nutritional status when used together with appropriate diet.