The number of adults with congenital heart disease (CHD) requiring diagnostic and/or therapeutic cardiac catheterization has been increasing. However, there have been few studies on the complications of performing cardiac catheterization in adults with CHD. The aim of this study was to determine the incidence of complications during congenital cardiac catheterization in both adults and pediatric patients. A total of 2134 consecutive cardiac catheterizations performed between 2003 and 2008 were prospectively analyzed. Complications were graded from 1 to 5 based on severity and these, with ≥ grade 3 being defined as major. During the study period, 576 procedures (393 diagnostic, 90 interventional, and 93 electrophysiological) were performed in adult patients (≥ 18 years). Complex heart disease was present in 435 of 576 procedures (75.6 %). A total of 65 complications (11.3 %) with 13 major complications including 1 death (2.3 %) were encountered. The most common complications were arrhythmias. The majority of complications were successfully treated or temporary, and all but one of the patients were without residua. Of the 1558 pediatric procedures performed during the same period, we found a total of 229 complications (14.7 %), of which 89 (5.7 %) were major complications including 5 deaths. The safety of performing cardiac catheterization for adult CHD appears to be similar to that for pediatric patients. The complication rates in adults with CHD are low, but not negligible.