This study aimed to explore the prevalence of overweight, obesity, and abdominal obesity, and define predictive factors of their occurrence among pre-adolescents in the region of Thrace, NE Greece. A secondary aim was to record physical activity at different times (schooldays, weekends, holidays) and explore associations with characteristics such as gender, overweight and obesity, and socio-demographic conditions. A cross-sectional study was conducted involving children aged 11–12 years. Participating children were measured for height, weight, and waist circumference, and their parents answered a questionnaire. In total, 1929 children were included. Prevalence of overweight was 31.5%, prevalence of obesity 17%, and only 1% of children were underweight. Abdominal obesity was detected in 20.3% of the sample. Overweight and obesity were more frequent in males, who also had higher mean values of Body Mass Index-for-age z-scores (BMIaz) and Waist-to-Height ratio (WtHR). Obesity rates were higher among those not participating in physical activities; however, no significant difference was observed between normal-weight, overweight and obese children in the time spent for organized athletic activities or free play. Logistic regression analysis showed that the probability for overweight/obesity was higher in boys (OR = 1.39, 95% CI = 1.16–1.66) and lower in children whose fathers had a higher educational level (OR = 0.75, 95% CI = 0.60–0.93). The probability for abdominal obesity was also higher in boys (OR = 1.37, 95% CI = 1.10–1.72) and lower in children participating at least one hour/day in an organized physical activity (compared to those with no physical activity (OR = 0.66, 95% CI = 0.51–0.85), and whose father was exercising at least 1–2 times/week (OR = 0.76, 95% CI = 0.591–0.98). In conclusion, the prevalence of overweight and obesity among pre-adolescents in NE Greece was estimated at 48.5%. This is associated with the male gender and not participating in physical activities. The educational level and exercise habits of the father (but not of the mother) affect the probability of obesity and abdominal obesity, respectively.