Dropout constitutes a chief obstacle to EFA in many developing countries including Cambodia. To prevent dropout, it is important to identify the reasons why children leave school. So far, much research has been conducted on the causes of school dropout mainly by asking stakeholders, especially dropped-out students and their parents to state their personal reasons why children are not in school. Unlike most of the previous studies, this study, in order to find out reasons more objectively and accurately, employed a longitudinal quantitative analysis. The study was conducted in five primary schools and five lower secondary schools in rural parts of Kampong Cham Province. The result of the follow-up study of three cohort groups showed that late school entry, repetition and low achievement were the main causes of dropout throughout the grades. To belong to some schools was another factor that influences student dropout decision. On the other hand, poverty which was mentioned as the main cause of dropout in many studies in Cambodia was found insignificant in this study.