The study was conducted to determine the family, social and economic factors associated with deaths of children aged under 5 years. A registry-based nested case-control study was conducted of the deaths of all children aged under 5 years in Kohgilooyeh and Boyer-Ahmad Province in the Islamic Republic of Iran. For each death, two controls were randomly selected among children of the same age, sex and place of residence (186 cases and 372 controls). Congenital abnormality (37.6%) and preterm birth (29.0%) were the two most frequent causes of death among children aged under 5 years. No vaccine-preventable disease was reported as the cause of death. The strongest associations were found with consanguinity of the parents (OR = 3.92; 95% CI = 2.27-6.85 for being first cousins in comparison with no family relation; P < 0.001) and with domestic violence to the mother during pregnancy (OR = 3.13; 95% CI = 1.60-6.17; P < 0.01). The main causes of death of children aged under 5 years in the Province were congenital abnormality and prematurity.