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We report the case of a 14-month-old female patient with a complete atrioventricular canal, phenotypically non-syndromic, who on admission presented a positive real-time (Polymerase chain reaction) PCR test for SARS-CoV-2, the novel virus that causes the COVID-19 pandemic, current context where much is still unknown regarding its clinical outcome and proper management, particularly in pediatric patients with pre-existing cardiac conditions. Atrioventricular septal defect is a complex congenital heart disease strongly associated with Down syndrome, characterized by a malformation during the development of the heart cross (crux cordis) or atrioventricular area. She is discharged with a referral to Cardiology. Despite her condition, the patient did not develop severe COVID-19 illness.