Introduction Refugee children in Western countries are considered to be at increased risk for child maltreatment. Data about asylum seeker children, however, are rare. The aim of our study was to assess the registered incidence of physical child maltreatment among asylum seekers in the Netherlands between 2000 and 2008, and associations with demographic and reception factors. Methods We used the electronic database of the community health services for asylum seekers, containing demographic, reception and health data of all asylum seekers in the Netherlands between 1 January 2000 and 31 December 2008. The study includes children <18&emsp14;years in reception with at least one parent (N=22 456). We used Cox regression analysis. Results The number of physical child maltreatment cases was 182. The registered incidence was 3.7 cases per 1000 person years. Multivariate Cox regression showed an increased risk for girls (RR=1.34; 95% CI 0.99 to 1.80) and children in single parent units (RR=1.72, 95% CI 1.25 to 2.37). Children born in reception have a lower incidence compared to children born before arrival. Those 12–18&emsp14;years at arrival had the largest risk (RR=2.69, 95% CI 1.57 to 4.59). Incidence differences were also found between countries of origin. The highest incidence was found for children from Iran and Former Yugoslavia (RR=1.49; 95% CI 0.84 to 2.65 and RR=1.30; 95% CI 0.72 to 2.34). Length of stay was not an independent risk factor. Conclusion Our study shows differences in the risk for physical child maltreatment between asylum seeker subgroups. Girls, children in single parent units and those with higher age at arrival are at increased risk. The results will contribute to priority setting in child maltreatment prevention.