We examined the association between overweight/gender and skipping breakfast among adolescent students in Tehran city using a cross-sectional study and a multistage random sampling method. All educational zones in Tehran city were covered during the educational year of 2000–01. In total, 2321 students aged 11–16 years (1068 male; 1263 female) participated in the study. Weight and height were measured and body mass index (BMI; kg/m2) was calculated. Overweight, pre-obesity and obesity were defined as BMI ≥ 85th, 85th to 95th, and ≥ 95th percentile of age-sex-specific BMI reference values, respectively. Self-reported frequency of breakfast consumption was categorized as usual/always, often, and rarely/never (5–7, 2–4 and 0–1 times/wk, respectively). Student’s t and Chi-square tests were employed to analyze the data. Statistical inferences were made at α = 0.05. In boys and girls, the mean ± standard deviation of BMI was 19.8 ± 4.0 and 20.6 ± 4.1 kg/m2, the 18.8% and 23.1% were overweight, and 7.3% and 8.3% were obese, respectively. There was a significant difference in the frequency of breakfast consumption between obese and normal male students (P < 0.001). Differences between pre-obese and normal, and obese and normal female students were also significant (P < 0.002 and P < 0.001, respectively). A significant difference was found in the frequency of breakfast consumption between male and female adolescents in all three categories (P < 0.001). These results suggest that obese and female adolescents are more likely to skip breakfast than their normal and male peers and are therefore at higher risk for growth deficits and low educational performance. Preventive/educational programs are urgently needed in this age group.