Background Numerous health problems are initiated in childhood and adolescence. For example, obesity, which has increased significantly in recent years, often begins in early life. The objective of this study is to describe social inequalities in obesity and other health problems among adolescents, by sex. Methods Data were from a cross-sectional study conducted in a representative sample of 903 adolescents aged 12–16 years old, from secondary schools in Barcelona, Spain. Associations between socioeconomic indicators and health outcomes (perceived health status, and overweight and obesity) were examined through generalised estimating equation models. All analyses were stratified by sex. Results Boys were more likely to report very good perceived health status than girls (64.1% and 46.3%, respectively). Some of the less privileged socioeconomic position indicators were associated with the presence of overweight and obesity (prevalence ratio 2.41 for low family affluence scale in girls), and with a lower probability of reporting very good perceived health status among boys (prevalence ratio 0.75 for primary level of paternal education). Conclusions This study suggests that there are social inequalities in perceived health status, overweight and obesity, measured by different socioeconomic indicators among the adolescent population of Barcelona, and that these inequalities were distributed differently among boys and girls. Gender differences in the impact of socioeconomic variables in health need to be considered in epidemiological and intervention studies.