The object of this study is to report on determinants of stunting, defined as low height for age, among children in the occupied Palestinian territories. Using 2006–2007 cross sectional survey data collected by the Palestine Central Bureau of Statistics and using multivariate mixed model techniques for logistic regression, the relationships of stunting to characteristics of 9,051 Palestinian children less than 5 years of age living in the Palestinian territories were estimated. These characteristics included demographic and social characteristics of the child, geographic region, type of location (urban, rural, refugee camp) and food insecurity for each governorate. Listed in order of the greater contribution to the explained variation in stunting, children with lower birth weight (P < 0.0001), age greater than 12 months (P < 0.0001), higher levels of food insecurity (P < 0.0001), lower socio-economic status (P < 0.0001), mother illiterate (P = 0.004), urban areas (P = 0.008), and absence of supplementation to breast feeding during the first 4 months of the child’s life (P = 0.04) have significantly more stunting. Children living in refugee camps have lower rates of stunting than urban areas; however the difference does not reach statistical significance. The relationship between the child’s gender and stunting is not statistically significant. Lack of food security is directly linked to stunting. The continuing incidence of food insecurity means that the deleterious effects of under-nutrition will continue to affect the children of Palestine. Removing the avoidable causes of food insecurity in the occupied Palestinian territories will alleviate under-nutrition and its deleterious effects.