Background: Childhood malnutrition is a multi-dimensional problem. An increase in household income is not sufficient to reduce childhood malnutrition if children are deprived of food security, education, access to water, sanitation and health services. The aim of this study is to identify the characteristics of malnourished children below five years of age and to ascertain the risk factors of childhood malnutrition in a state in Malaysia. Methods: A case control study was conducted in the maternal and child health clinics in five districts of Terengganu, Malaysia from April to August 2012. Case was a child with moderate to severe malnutrition with z-scores < -2SD from the median of WHO reference. Control was a child without malnutrition with z-scores between -2SD and +2SD and the age matched with case's. Face to face interviews with the respective child's mother and measurements of the respective child's weight and height were carried out. Information on socio-economic characteristics, household food security status, child's dietary intake, caregivers' practices and resources were enquired. Univariate and multivariate logistic regression analyses were conducted. Crude odds ratio and adjusted odds ratio with 95% confidence interval were calculated. Results: A total of 274 children with 137 cases and 137 controls were recruited. All respondents were Malays. Among the cases, a larger proportion of them was female and originated from low income families. After adjusting all confounders, childhood malnutrition was significantly associated with number of children (aOR: 5.86, 95% CI: 1.96, 17.55), child hunger (aOR: 16.38, 95% CI: 1.34,199.72), dietary energy intake (aOR: 0.99, 95% CI: 0.98, 0.99), protein intake (aOR: 1.06, 95% CI: 1.01, 1.12), vitamin A intake (aOR: 0.999, 95% CI: 0.997, 1.00), low birth weight (aOR: 6.83, 95% CI: 1.62, 28.89), frequent illness (aOR: 2.79, 95% CI: 1.06, 7.31), and history of worm infection (aOR: 3.48, 95% CI: 1.25, 9.70). Conclusions: Lower socio-economic status, household food insecurity, and poor child caring practices were associated with childhood malnutrition. Besides implementation of programmes focusing on poverty reduction, community based nutrition and hygiene education with extensive family planning and de-worming programmes should be intensified to improve both mother and children's nutritional status. [ABSTRACT FROM AUTHOR]