Objective: Divorce as a phenomenon leading to instability of the families can affect children’s life in different aspects, and have been studied in different researches. This study is on mental health and self-esteem of children from intact families, children under paternal custody and children under maternal custody. Method: In this study ninety students (boys) in three groups of thirty from Islamshahr junior high schools were chosen (boys under paternal custody and boys under maternal custody and boys from intact families) and careful attention was paid to matching The tools in this study were Cooper Smith self-esteem questionnaire (adolescence form) and General health questionnaire (GHQ-28). Findings: The result demonstrated a higher degree of self-esteem and mental health in children from intact families then in children from divorced families (both for paternal custody or maternal custody). Taking about self-esteem although, there weren't any considerable differences between boys under paternal custody and those who were under maternal custody, but the total of mental health score in the second group (e.g. boys under maternal custody) was more than the former one. Furthermore, the subscales in the first group have gotten higher ranks.