Objective: Congenital heart disease (CHD) plays a key role in oral and dental health regarding its own impacts on teeth (i.e., enamel hypoplasia), infective endocarditis and choice of dental treatment. The purpose of this study’s comparing the oral and dental health status in children with or without CHD is to contribute to the literature by determining the effects of CHD on oral and dental health. Material and Methods: The present study was conducted using a descriptive and correlational design and consisted of 581 children aged between 6 months and 18 years who were healthy (n = 364) or experienced CHD (n = 217). CHD-impacted children were classified according to their shunt and stenosis and then their saturation values were noted. In the intraoral examination, caries data (dmft/DMFT, PUFA/pufa), oral hygiene (OHI-S) and enamel defect (DDE) indices were recorded. Statistical analyses were performed using SPSS 26.0 at a significance level of 0.05. Results: In our study, caries index scores of children with or without CHD in primary or permanent dentition were found to be similar. The mean OHI-S index (p < 0.001) and gingivitis findings (p = 0.047) of children with CHD had a higher prevalence than the healthy ones. The incidence of enamel defects was determined as 16.5% in CHD-affected children whereas an incidence rate of 4.7% was observed in healthy children. The mean saturation value of the participants with enamel defects (89 ± 8.9) was observed to be significantly lower (p = 0.03) than the patients with no enamel defects (95 ± 4.2). Conclusions: Whereas the caries index scores of CHD-affected children with a history of hypoxia in primary and permanent dentition were found to be similar to the healthy ones, children with CHD were observed to be more prone to enamel defects and periodontal diseases. Furthermore, considering the risk of infective endocarditis resulting from existing carious lesions and periodontal problems, it is highly important for pediatric cardiologists, pediatricians and pediatric dentists to collaborate in a multidisciplinary manner.