The aim of this study was to estimate the prevalence and identify the risk factors of hepatitis C virus (HCV) infection among healthy Egyptian children. A representative random sample of 500 children, age between 6 and 15 years, was selected from 10 schools in Alexandria, Egypt. A questionnaire was used to collect demographic data and potential risk factors, while blood samples were collected and analyzed for antibodies to HCV (anti-HCV). Positive sera were further confirmed by HCV-RNA. HCV seroprevalence of 5.8% was found, with HCV viraemia in 75% of the studied children. The prevalence of anti-HCV increased with age from 0% in children aged 6–7 years to 16% in those of 15 years old. It was also shown that history of previous blood transfusion (odds ratio[OR] = 34.8, 95% CI = 4.39–272.95), intravenous injections (OR = 4.68, 1.89–11.59), surgical intervention (OR = 5.64, 2.55–12.52), dental treatment (OR = 6.81, 2.64–17.39), injection (OR = 2.29, 1.08–4.89) and circumcision for boys by informal health care providers (OR = 2.6, 1.0–6.73), age above 10 years (OR = 6.83, 2.44–19.07), very low socioeconomic class (OR = 5.92, 1.3–25.2) and rural area residence (OR = 2.49,1.61–5.29) are the most significant risk factors for HCV infection. Adjusting for all other risk factors by multivariate logistic regression analysis, it has been shown that blood transfusion, surgical procedures, dental treatment, and age above 10 years are still significant risk factors associated with anti-HCV (P < 0.05). The current study reveals the extremely high HCV seroprevalence among Egyptian children. This mandates immediate preventive strategies to limit further HCV spread.