Background Childhood malnutrition as a major public health problem among children in developing countries can affect physical and intellectual growth and is also considered as a main cause of child morbidity and mortality. The objective of this study was to estimate the prevalence of under-nutrition and identify determinants of malnutrition among children under ۶ years of age in Fars province, Iran. Methods This survey was conducted by house to house visit through multi-stage sampling in ۳۰ cities of Fars province, during December ۲۰۱۲ to January ۲۰۱۳. A total of ۱۵۴۰۸ children, aged ۰–۶ years old, were studied for nutritional assessment in terms of underweight, stunting, and wasting. Also, socio-demographic measures were obtained from structured questionnaire. Backward stepwise logistic regression was used to relate underlying factors to the odds of under-nutrition indices. Results The rates of stunting, underweight, and wasting were ۹.۵۳, ۹.۶۶, and ۸.۱۹%, respectively. Male children were more stunted compared to females (OR= ۱.۴۱, CI: ۱.۲۶–۱.۵۸). Also, stunting was significantly associated with lower family income (OR= ۳.۲۱, CI: ۱.۱۷–۸.۸۵) and lower maternal education (OR= ۰.۸۰, CI: ۰.۶۴–۰.۹۸). Living in urban areas, and poor water supply were identified as significant risk factors of all three types of childhood under-nutrition. Moreover, Khamse and Arab ethnic groups were more vulnerable to under-nutrition. There was a suggestion that non-access to health services were associated with wasting (OR= ۱.۸۷, CI: ۱.۳۹–۲.۵۲) and also large family size was related to underweight (OR= ۱.۳۵, CI: ۱.۱۰–۱.۶۵). Conclusion The prevalence of under-nutrition in the study population was categorized in low levels. However, planning the public preventive strategies can help to control childhood under-nutrition according to underlying factors of malnutrition in the study population including gender, settlement area, family size, ethnicity, family income, maternal education, health services, and also safe water supply.
