Background Children’s exposure to violence is a major public health issue. The Balkan epidemiological study on Child Abuse and Neglect project aimed to collect internationally comparable data on violence exposures in childhood. Methods A three stage stratified random sample of 42,194 school-attending children (response rate: 66.7%) in three grades (aged 11, 13 and 16 years) was drawn from schools in Albania, Bosnia and Herzegovina, Bulgaria, Croatia, Former Yugoslavian Republic of Macedonia (FYROM), Greece, Romania, Serbia and Turkey. Children completed the ICAST-C questionnaire, which measures children’s exposure to violence by any perpetrator. Results Exposure rates for psychological violence were between 64.6% (FYROM) and 83.2% (Greece) for lifetime and 59.62% (Serbia) and 70.0% (Greece) for past-year prevalence. Physical violence exposure varied between 50.6% (FYROM) and 76.3% (Greece) for lifetime and 42.5% (FYROM) and 51.0% (Bosnia) for past-year prevalence. Sexual violence figures were highest for lifetime prevalence in Bosnia (18.6%) and lowest in FYROM (7.6%). Lifetime contact sexual violence was highest in Bosnia (9.8%) and lowest in Romania (3.6%). Past-year sexual violence and contact sexual violence prevalence was lowest in Romania (5.0 and 2.1%) and highest in Bosnia (13.6 and 7.7% respectively). Self-reported neglect was highest for both past-year and lifetime prevalence in Bosnia (48.0 and 20.3%) and lowest in Romania (22.6 and 16.7%). Experiences of positive parental practices were reported by most participating children in all countries. Conclusions Where significant differences in violence exposure by sex were observed, males reported higher exposure to past-year and lifetime sexual violence and females higher exposure to neglect. Children in Balkan countries experience a high burden of violence victimization and national-level programming and child protection policy making is urgently needed to address this. Electronic supplementary material The online version of this article (10.1186/s13034-017-0208-x) contains supplementary material, which is available to authorized users.