Background In 2012, the prevalence of obesity and overweight statuses among children in Spain was 9% and 26%, respectively. Concerns about childhood obesity have increased over the past few years, as obesity developed during childhood can persist throughout an individual's lifetime (cohort effect). This study aims to develop a better understanding of the factors influencing the prevalence of obesity in Spain. Methods Microdata from the 2012 National Health Survey are used, and the methodological framework is based on the estimation of a sample selection model. Results Results suggest that the prevalence of obesity increases among children who live in households of a lower socio-economic status and households in which parents are obese. Lower levels of childhood physical activity are positively related to the probability of being obese. Finally, there exists a positive relationship between children's body mass index and an inappropriate intake of fresh fruits, fish, pasta and rice, legumes, sweets and soft drinks. Conclusions The methodological framework used in this study is flexible enough to be used in traditional longitudinal studies. Children's and households' lifestyles play a pivotal role in the prevalence of obesity. Policies should be oriented toward changing lifestyles, which would require more multidisciplinary research in the future to reduce childhood obesity.