The prevalence and risk factors of hepatitis A, B, and C (HAV, HBV, and HCV) markers were compared in non-Roma and Roma children who lived in a deprived suburb of Athens, Greece. The study included 216 children, 118 Roma and 98 non-Roma of 9 years median age (range 5-15 years). Among Roma children 98.3% had detectable antibodies to HAV, compared with 32.7% among non-Romas (P < 0.0001). Regarding HBV, 22% Roma children were identified with evidence of past infection (anti-HBc(+)), among whom five (4% of the total) were chronic carriers (HBsAg(+)), whereas no past infection was detected among the non-Romas (P < 0.0001). Markers of past HBV vaccination (anti-HBs(+), anti-HBc(-)) were detected in only 14% Roma but 96% non-Roma children (P-value < 0.0001). There was some indication for intrafamilial transmission of HAV and HBV in Roma school children. Unfavorable living conditions, frequent residency change, lack of child insurance and primary healthcare delivery were significantly associated with seroprevalence of HBV infection among Romas. No child in either group was found positive for HCV markers. These findings document high socioeconomic differentials with regards to preventable communicable diseases, such as HAV and HBV and underline the need for enhancing health policy action targeting pockets of minority childhood populations. Whereas, uptake of HBV vaccination is rather optimal in this general population, the high seroprevalence of HAV among Romas, also calls for implementing general vaccination for HAV, early in life.