Abstract Background The highest prevalence of several cardiovascular disease risk factors including obesity, smoking and low physical activity level is observed in adults of low socioeconomic status. This study investigates whether tracking of body mass index and physical fitness from childhood to adolescence differs between groups of socioeconomic status. Furthermore the study investigates whether social class differences in the prevalence of overweight and low physical fitness exist or develop within the age range from childhood to adolescence. Methods In all, 384 school children were followed for a period of six years (from third to ninth grade). Physical fitness was determined by a progressive maximal cycle ergometer test and the classification of overweight was based on body mass index cut-points proposed by the International Obesity Task Force. Socioeconomic status was defined according to The International Standard Classification of Occupation scheme. Results Moderate and moderately high tracking was observed for physical fitness and body mass index, respectively. No significant difference in tracking was observed between groups of socioeconomic status. A significant social gradient was observed in both the prevalence of overweight and low physical fitness in the 14–16-year-old adolescents, whereas at the age of 8–10 years, only the prevalence of low physical fitness showed a significant inverse relation to socioeconomic status. The odds of both developing and maintaining risk during the measurement period were estimated as bigger in the group of low socioeconomic status than in the group of high socioeconomic status, although differences were significant only with respect to the odds of developing overweight. Conclusion The results indicate that the fundamental possibilities of predicting overweight and low physical fitness at an early point in time are the same for different groups of socio-economic status. Furthermore, the observed development of social inequalities in the absolute prevalence of overweight and low physical fitness underline the need for broad preventive efforts targeting children of low socioeconomic status in early childhood.