Parents of children with congenitally malformed hearts can suffer from stress as a result of the medical condition of their child. In this cross-sectional study, we aimed to describe levels of parental stress, and perceived vulnerability, in parents of children who underwent major cardiac surgery, by using both generic and disease-related measures for assessment. We included parents of children who underwent open-heart surgery over the period 2002 through 2007 in the Center for congenital Anomalies Heart Amsterdam/Leiden, abbreviated to provide the acronym CAHAL. In total, we assessed 114 mothers and 82 fathers of 131 children, using the Pediatric Inventory for Parents, short form, General Health Questionnaire, Parental Stress Index-Short Form, State-Trait Anxiety Index and the Child Vulnerability Scale. Compared to the reference groups of the instruments used, parents of children with congenitally malformed hearts did not report higher generic nor disease-related stress scores, and parenting levels of stress were also comparable to reference groups. State anxiety levels, however, were higher in mothers of children with congenitally malformed hearts. Both fathers and mothers reported significantly higher rates of perceived vulnerability than did parents of healthy children. Risk factors for increased anxiety and perceived vulnerability were found in the number of surgical procedures, the time past since the last procedure, and ethnicity. Severity of the lesion did not influence parental levels of stress, but parents of children with hypoplastic left heart syndrome did report higher levels of stress than other parents. Psychosocial screening of parents of children with congenitally malformed hearts is important in order to provide appropriate counselling to those parents most in need.