Background Pediatric heart transplant recipients exhibit cognitive delays, as evident in assessments of their general intelligence. Less is known about their specific neurocognitive impairments. Methods All 19 children in Finland aged 6 to 16 years who had undergone heart transplantation (HTx) participated. Of these, 12 (63%) had cardiomyopathy (CM) and 7 (37%) had congenital heart disease (CHD). They were assessed on average 5.5 (SD, 3.6) years post-operatively at a mean age of 12.0 (SD, 3.1) years. A standardized test of intelligence (Wechsler Intelligence Scale for Children [WISC]-III), a neuropsychological test battery (NEPSY-II), and a parental developmental questionnaire (FTF) were administered. The neuropsychological test profile of the HTx group was compared with that of a matched control group. Results HTx children had a lower mean Performance Intelligence Quotient (PIQ; 82.2, p = 0.001) and Full-Scale IQ (FSIQ; 85.6, p = 0.004) compared with population norms. HTx children scored generally lower than the control group on the neuropsychological tests (p = 0.002). Seven patients with pre-HTx neurologic sequelae (n = 6) or extreme prematurity (n = 1) had lower mean FSIQ (72.1) than did children without major pre-HTx risk factors (93.5, p = 0.012). The latter group scored below average on only 1 of 6 WISC-III sub-tests and 2 of 10 NEPSY-II sub-tests, all measuring visuoconstructional performance. Conclusions Children without major neurologic risk factors pre-HTx may have normal general intelligence after HTx but deficits in the visuoconstructional domain.