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Being overweight and obese during childhood increases the potential of becoming obese adults later in life. Therefore, this study aims to determine the factors associated with overweight (including obesity) among children under five years of age in Putrajaya, Malaysia. A total of 211 children with overweight cases were successfully recruited in this case-control study. The same number for control group which was normal children also being recruited by matching according to sex and age group with the case group. Data collection was performed by four approaches such as face-to-face interview, anthropometric measurements, finger prick for haemoglobin level and self-administered 3-day food diary. WHO Anthro software was used to determine the nutritional status of children. Descriptive statistic and logistic regression were performed to determine risk factors that contributed to overweight. Multiple logistic regressions showed overweight or obese father was 1.88 times more likely to have overweight children compared to normal BMI father. Mothers who had gestational diabetes mellitus (GDM) were 2.93 times more likely to have overweight children compared to those with no complication during pregnancy. Pregnant women who attended antenatal visits for less than 9 times were 3.33 times more likely to have overweight children compared to pregnant women who attended 9 to 14 times of antenatal visits. Children with fewer siblings were 2.10 times more likely to be overweight compared to children with four or more siblings. These findings indicated related risks factors contributing to childhood overweight from the early stages including maternal and paternal factors. Early life intervention especially during pregnancy stages which include antenatal care and antenatal intervention on dietary and physical activity during peri-conception period is seen to be important to prevent adverse pregnancy outcomes and further improve maternal and child’s health. Hence it would be more effective to prevent childhood overweight or obesity in later age and its long-term consequences.