Oral bacteria and odontogenic oral infections are responsible for a high portion of cases with infective endocarditis. Hence, oral health in patients with congenital heart disease (CHD) gains particular importance. This case-control study compared the oral health status in 112 adults with CHD and 168 healthy control subjects. In addition, the patient group was stratified according to the complexity of the heart defect and the recommendation for antibiotic prophylaxis during invasive dental procedures. Considering caries experience, a significantly lower mean DMFT (decayed missing filled teeth) score (7.91 ± 6.63 vs. 13.6 ± 8.15; p < 0.0001) was found in patients with CHD compared to healthy controls. Healthy controls had a higher average number of decayed teeth (0.33 ± 0.76 vs. 1.76 ± 2.61; p < 0.0001). In female subjects a significant lower relative amount of teeth with apical periodontitis was found among CHD patients (3.4% ± 0.9%) as compared to healthy controls (5.6% ± 1.9%) (p = 0.053). Regarding periodontal health, patients with CHD had lower rate of sulcus bleeding (0.32 ± 0.65 vs. 0.71 ± 0.60; p < 0.0001) and less alveolar bone loss than heart healthy individuals (% root length: multi rooted teeth: 8.97 ± 10.64 vs. 23.22 ± 20.70; p < 0.0001; single rooted teeth: 5.59 ± 6.25 vs. 17.30 ± 17.17; p = 0.003). On the contrary, CHD patients presented with higher amount of plaque in comparison to healthy controls (Quigley & Hein index: 2.22 ± 0.67 vs. 1.25 ± 0.72; p < 0.0001). Based on the current results, it can be concluded that adults with CHD have better oral health than heart healthy individuals.