Aim: The aim of this study is to measure objectively and accurately the physical activity (PA) patterns in Spanish children and adolescents according to their obesity status, gender and age groups. Methods: A sample of 487 children and 274 adolescents from the European Youth Heart Study participated in the study. The variables measured were anthropometric characteristics (height, weight and body mass index), and PA was measured during 6 consecutive days using the GT1M accelerometer. Results: Three-way analysis of variance (age x gender x obesity status) showed significant differences in the interaction effect in age, gender and obesity status (normal-weight and overweight/obesity) for mean of moderate-to-vigorous PA (MVPA) (P = 0.02) and vigorous PA (VPA) (P = 0.014) within the sample. Nine-year-old normal-weight children achieved significantly (P < 0.05) more MVPA on weekdays than 9-year-old overweight/obesity children. During weekend days, all sample achieved significant moreMVPA (P < 0.01) and significant more VPA (P < 0.05) than during weekdays. Few children (37.5% of 9-year-old normal-weight and 34.0% of 9-year-old overweight/obese) and adolescents (16.4% and 27.3% normal-weight and overweight/obese, respectively) met the current health-related recommendations of 60 min of MVPA daily. Conclusions: It is clear that activity levels are insufficient for all children, in particular overweight/obese children and adolescents, although the precise nature of the relationship appears to differ between boys and girls.