Objective: To describe the prevalence of overweight, analyze its progression from 1989 to 2006 and identify factors associated with it among children younger than two years in Brazil. Methods: Data for the Women and Children National Demography and Health Survey (PNDS 2006) were collected using questionnaires and anthropometric measurements. The study sample included 1,735 children aged 0 to 24 months (910 boys; 825 girls). Nutritional status was defined according to the weight-for-height index (W/H; WHO, 2006), and children were classified as overweight if their W/H z score was greater than +2. Results: Prevalence of overweight in Brazil was 6.54%. The highest prevalence of overweight was found in the southern (10.0%) and midwestern (11.1%) regions, among families with a per capita income higher than one minimum wage (11.8%), in social classes with a greater purchasing power (9.7%), among children whose birth weight was greater than 3 kg (8.04%) and whose exclusive breastfeeding lasted less than five months (7.4%). According to a fitted multiple logistic regression model, factors associated with overweight were: birth weight ≥ 3 kg [odds ratio (OR) = 5.2, 95% confidence interval (95%CI) 2.56-10.56], per capita income ≥ 1 minimum wage (OR = 2.50, 95%CI 1.20-5.21), residence in midwestern region (OR = 2.40, 95%CI 1.01-5.72). Conclusions: The comparison of the prevalence found in the 2006 survey with the 1989 and 1996 values revealed that overweight among children younger than two years tends to decrease. The risk factors identified suggest that further actions should be conducted to prevent obesity among infants living in the midwestern region of Brazil, whose birth weight was greater than 3 kg and whose families had a per capita income higher than one minimum wage. 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