Introduction: Water fluoridation (WF) was ceased in the state of Pahang, Malaysia, in July 2012. Any changes in fluoride exposure during childhood can influence the development of fluorosis. Thus, this study aimed to compare the prevalence of fluorosis between WF-ceased and WF-continued areas in Malaysia, and its associated factors among 7 and 12-year-old children. Methods: A cross-sectional study was conducted among children in WF-ceased and WF areas (n=1211). The 12-year-olds in WF-ceased areas were exposed to WF between 4.5 to 6.5 years before cessation, and it was hypothesised they would have similar fluorosis prevalence as their counterparts who lived in WF areas. The 7-year olds were born during the cessation period. Examination of fluorosis was performed by a calibrated dentist using Dean’s criteria and a parental questionnaire was utilised to collect information about demographics and exposure to fluoride. Results: Fluorosis prevalence (Dean’s≥2) was significantly lower among children in WF-ceased areas than WF areas (p< 0.001). Intra-area comparison indicated that the 12-year olds have higher prevalence of fluorosis than the 7-year-olds, except for anterior fluorosis scores among those in WF areas. The majority of fluorosis cases were very mild in both areas. Simple logistic regression indicated that duration of exposure to WF, age, mother’s income and education, age started toothbrushing with toothpaste, and frequency of toothbrushing were associated with fluorosis. Conclusions: Fluorosis prevalence decreased following water fluoridation cessation. The null hypothesis that 12-year-olds in both areas would have similar prevalence of fluorosis was rejected. Several factors were associated with fluorosis.