We conducted a hospital-based cross-sectional study among children aged <5 years in Thi-Qar Governorate, south-eastern Iraq, in order to examine the prevalence, risk factors and antimicrobial resistance associated with gastroenteritis caused by Salmonella infection. From 320 diarrhoea cases enrolled between March and August 2016, 33 (10·3%, 95% confidence interval (CI) 8·4–12·4) cases were stool culture-positive for non-typhoidal Salmonella enterica. The most commonly identified serovar was Typhimurium (54%). Multivariable logistic regression analysis indicated that the odds of Salmonella infection in children from households supplied by pipe water was 4·7 (95% CI 1·6–13·9) times higher compared with those supplied with reverse osmosis treated water. Similarly, children from households with domestic animals were found to have a higher odds (OR 10·5; 95% CI 3·8–28·4) of being Salmonella stool culture-positive. The likelihood of Salmonella infection was higher (OR 3·9; 95% CI 1·0–6·4) among children belonging to caregiver with primary vs. tertiary education levels. Lower odds (OR 0·4; 95% CI 0·1–0·9) of Salmonella infection were associated with children exclusively breast fed as compared with those exclusively bottle fed. Salmonella infection was three times lower (95% CI 0·1–0·7) in children belonging to caregiver who reported always washing hands after cleaning children following defecation, vs. those belonging to caregivers who did not wash hands. The antimicrobial resistance profile by disc diffusion revealed that non-susceptibility to tetracycline (78·8%), azithromycin (66·7%) and ciprofloxacin (57·6%) were the most commonly seen, and 84·9% of Salmonella isolates were classified as multi-drug resistant. This is the first study on prevalence and antimicrobial resistance of Salmonella infection among children in this setting. This work provides specific epidemiological data which are crucial to understand and combat paediatric diarrhoea in Iraq.