The study identified 11 factors that contribute to stunting in children under 5 years old in Putrajaya, Malaysia. The strongest associated factor was complications during pregnancy like intrauterine growth restriction. Other significant factors included mid-parental height less than 150cm, low household income, low birth weight, use of pacifiers, lower maternal education, unemployed fathers, anemia in children, bottle feeding, lack of minimum dietary diversity, and care by babysitters. Addressing these maternal, socioeconomic, childcare and nutritional factors through community interventions and policies could help reduce the high prevalence of stunting in Putrajaya.