Breakfast is considered as the most important meal of the day. The habit of skipping this meal in adolescence tends to remain until adulthood and has been associated with cardiometabolic risk factors. The present study estimated the prevalence of skipping breakfast and its association with cardiometabolic risk factors. This is a cross-sectional study with data from the Study of Cardiovascular Risks in Adolescents (ERICA), with a nationally representative sample of 36 956 Brazilian adolescents, aged 12–17 years, enrolled in public and private schools. The outcomes were excess body weight (BMI), central obesity (waist circumference and waist:height ratio), lipid profile (total cholesterol (TC), LDL-cholesterol, HDL-cholesterol and TAG) and glycidic profile (fasting glycaemia, fasting insulin and glycated Hb). The association between skipping breakfast and each outcome was estimated using multiple Poisson regression models (prevalence ratio (PR) and 95 % CI). Prevalence of skipping breakfast was 68·7 % and, after adjustments, it was associated with excess body weight (PR = 1·30; 95 % CI 1·18, 1·43), central obesity both by waist circumference (PR = 1·27; 95 % CI 1·00, 1·61) and by waist:height ratio (PR = 1·32; 95 % CI 1·13, 1·54) and high fasting glucose levels (PR = 1·54; 95 % CI 1·09, 2·18), fasting insulin (PR = 1·64; 95 % CI 1·21, 2·22), glycated Hb (PR = 1·16; 95 % CI 1·03, 1·31) and total cholesterol (PR = 1·14; 95 % CI 1·02, 1·27). Skipping breakfast was associated with cardiometabolic risk factors in adolescence. In this context, the school environment is an ideal space to promote healthy eating habits, favouring the implementation of food and nutrition education activities to make adolescents aware of the importance of consuming breakfast daily.