Children with multisystem involvement including congenital heart defect (CHD) are a very salient problem. The purpose of this study was to evaluate the incidence of CHD associated with malformations of other systems and to assess the modalities of treatment and perioperative mortality among patients referred to the department of pediatric cardiac surgery. The medical records of 1856 children were reviewed retrospectively from 1997 to 2002 to establish CHD and types of associated malformations. The connections between CHD and other lesions were investigated. Furthermore, the influence of patient and perioperative variables on mortality risk was scrutinized. Univariate and multivariate analyses were used. Eighty-four children (4.53%) had CHD and associated malformations. The malformations of digestive (35.7%), urinary (22.4%), and nervous (14.3%) systems were the most frequently observed associated defects. No relation was found between CHD and concomitant lesions. The results of multivariate logistic regression showed significant influence of patient age, primary cardiac procedure, and CHD type on mortality (ca 19%) in children with multiorgan lesions. The treatment of children with CHD and associated multiple lesions is connected with higher mortality risk. The following factors: younger age, urgency of surgical procedure, and primary surgical procedure had negative impact on patient's outcome. However, these risks in certain cases are inevitable. The cardiac procedure preceding the surgical operation may improve the overall effect of treatment because of circulatory stabilization, provided that the condition of the patient does not preclude any intervention at all.