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Background and study aims The coronavirus disease 2019 (COVID-19) pandemic has had considerable effects on health care services given the need for re-allocation of resources and interruption of medical care. COVID-19 poses a challenge to patients with liver disease who are at risk of infection and more severe disease course. The current study aimed to assess the incidence of COVID-19 in children with liver diseases and evaluate the extent to which health care delivery was affected during lockdown. Patients and methods This cross-sectional analytical study conducted at the Pediatric Hepatology Unit, Cairo University Children’s Hospital utilized a questionnaire to determine the incidence of COVID-19 in patients with liver diseases and the impact of COVID-19 on the patients’ liver condition and health care service delivery. A presumed score was implemented to identify patients with probable COVID-19. Results Data from 349 children with liver diseases were analyzed. The overall incidence of COVID-19 was 8%. Patients with documented and probable COVID-19 were compared to improbable COVID-19 cases. Notably, COVID-19 cases were younger and had higher incidence rates of cholestatic liver diseases. COVID-19 patients experienced significantly higher rates of hepatic complications (43%) and had significantly greater need for medical services during the lockdown. All COVID-19 patients recovered after a median (IQR) duration of 3 (4) days, except for one patient who succumbed to COVID-19 and hepatic complications. Conclusions COVID-19 affected the younger hepatic patients with cholestatic disorders of infancy. Hepatic complications were more common among COVID-19 infected children. Alternative ways of communication require development to prioritize patients who needs a hospital visit and monitoring. Clinical scores may help diagnosis of COVID-19 in low/middle income countries like Egypt to compensate for the deficient laboratory diagnostic facilities.