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The aim of the current work was to evaluate the effect of preschoolers' television (TV) watching time on the prevalence of obesity even after controlling for their total energy intake and their physical activity status. A representative sample of 2,374 Greek children aged 1–5 years was examined (“Growth, Exercise and Nutrition Epidemiological Study in preSchoolers”, GENESIS study). Children's TV watching time on a usual weekday and at a usual weekend was recorded. The overall mean of children's TV viewing time was 1.32 h/day. The majority of participants (74.0%) spent <2 h/day watching TV whereas only 3.1% spent >4 h/day in front of a TV set. Overall, 65.2% of participants were normal weight, 17.2% were overweight, and the rest 17.6% were obese. The prevalence of obesity was significantly higher among those with TV viewing time ≥2 h/day (21.7%) compared to those watching TV <2 h/day (16.1%, P = 0.003). TV viewing time remained significantly associated with the likelihood of being obese even after controlling for potential confounders (i.e., socio demographic and other characteristics and physical activity status) only among children aged 3–5 years. However, further adjusting for children's total energy intake revealed that the association between the TV viewing time and the probability of being obese was no longer statistically significant. On the other hand, physical activity status continued to be an independent factor of being obese. The current findings support the hypothesis that the effect of TV viewing time on childhood obesity is independent of physical activity status and may be attributed to the increased total energy intake during TV watching.