<b><i>Introduction:</i></b> Autosomal dominant polycystic kidney disease (ADPKD) is caused mainly by pathogenic variants in <i>PKD1</i> or <i>PKD2</i> encoding the polycystin-1 and -2 proteins. Polycystins have shown to have an essential role in cardiac development and function in animal models. In the current study, we describe the clinical association between ADPKD and congenital heart disease (CHD). <b><i>Methods:</i></b> Medical records from Mayo Clinic were queried for all patients with confirmed ADPKD and CHD between 1993 and 2020. CHD was categorized into left-to-right shunt, obstructive, and complex lesions. Patent foramen ovale, mitral valve prolapse, and bicuspid aortic valve anomalies were excluded. <b><i>Results:</i></b> Twenty-five out of 1,359 (1.84%) ADPKD patients were identified to have CHD. Of these, 84% were Caucasians and 44% were males. The median (Q1–Q3) age (years) at CHD diagnosis was 12.0 (2.0–43.5). Fourteen patients (56%) had left-to-right shunt lesions, 6 (24%) had obstructive lesions and 5 (20%) complex lesions. Seventeen patients (68%) had their defects surgically corrected at a median age (Q1–Q3) of 5.5 (2.0–24.7). Among 13 patients with available genetic testing, 12 (92.3%) had <i>PKD1</i> pathogenic variants, and none had <i>PKD2</i>. The median (Q1–Q3) age at last follow-up visit was 47.0 (32.0–62.0) and median (Q1–Q3) eGFR was 35.8 (11.4–79.0) mL/min/1.73 m². Three patients (12%) died; all of them had left-to-right shunt lesions. <b><i>Discussion/Conclusion:</i></b> We observed a higher CHD frequency in ADPKD than the general population (1.84 vs. 0.4%). While only <i>PKD1</i> pathogenic variants were identified in this cohort, further studies are needed to confirm this novel finding and understand the role of polycystins in the development of the heart and vessels.