In this study, 31 (30%) cases of urinary tract infection (UTI) of 103 patients with malnutrition, who were admitted to our hospital, were investigated prospectively. Our purpose was to determine the frequency of UTI, species of bacteria caused to infection and their antibiotic susceptibility in infants with malnutrition. The mean age of the patients with UTI was 11.5+/-7.6 months (ranging 50 days-30 months). The main symptoms were fever, vomiting, diarrhea, cough, and seizures. The mean body weight was 5.8+/-1.9 kg (2-10 kg), and height was 67.5+/-7.8 cm (53-85 cm). Seven of them had mild, 11 had moderate, and 13 had severe malnutrition. The most common isolated microorganism from urine cultures was Escherichia coli (54.8%). Most strains of Escherichia coli were resistant to co-trimoxazole (82.3%), ceftriaxone (17.6%), cefotaxime (17.6%), and ciprofloxacine (17.6%), but none of them were resistant to gentamicin. In conclusion, we would like to emphasize that UTI predominantly by gram negative microorganisms are frequent in the infants with malnutrition, and these microorganisms are mostly resistant to co-trimoxazole which is used commonly in practical medicine and prophylaxis.