Introduction: The quality of relationship between children and parents in the early years of life is one of the most effective factors in the mental growth of the children. A parent being affected by schizophrenia may have very deep effects on the mental growth of the children. This study aimed to compare the behavioral problems in the children with one schizophrenic parent and children with healthy parents. Material and methods: This descriptive study was performed in Zahedan, Iran in 2014-2015. The behavioral problems of 60 children with a schizophrenic parent were compared to that of 60 children with healthy parents. The Child Behavior Checklist (CBCL) was used to evaluate the two groups. Results: The comparison of the CBCL score between two groups showed a significant difference (P < 0.005). Moreover, the CBCL score of primary school girls (P = 0.03) and boys (P = 0.04) was significantly different between the two groups. No significant difference was reported between the two groups regarding the CBCL score of teenage girls (P = 0.09) and teenage boys (P = 0.09). Conclusions: Our findings can be regarded as evidence supporting the effect of psychotic disorders, such as schizophrenia in parents on the behavioral problems of children.