Objective: To evaluate the incidence of cancer within the first 15 years of life in children who underwent cardiac catheterization under the age of one year. Methods: In this retrospective, single center study, 2770 infants (7.8% with trisomy 21) were studied. All infants underwent cardiac catheterization under one year of age between January 1980 and December 1998. Newly diagnosed cancer in the first 15 years of life was assessed through record linkage to the German Childhood Cancer Registry (GCCR). Cancer risk in study patients was compared to the GCCR population of children less than 15 years. Patients with trisomy 21 were compared to the Danish Cytogenic Register for trisomy 21. Effective radiation doses were calculated for each tumor patient and 60 randomly selected patients who did not develop cancer. Results: In total, 24,472.5 person-years were analyzed. Sixteen children developed cancer, while 3.64 were expected (standardized incidence ratio (SIR) = 4.4, 95% confidence interval (CI): 2.5−7.2, p < 0.001). There was no preferred cancer type. The observed incidence of leukemia and solid tumors in trisomy 21 was only slightly higher (1 in 476 py) than expected (1 in 609 py, p = 0.64). There was no direct relationship between the radiation dose and the incidence of cancer. Conclusion: Cardiac catherization in the first year of life was associated with a significantly increased cancer risk in a population with congenital heart disease.