Background Efforts to explain social inequalities in health have mainly focused on adults. Few studies have systematically analysed different explanatory pathways in adolescence. This study is among the first to examine the contribution of material, psychosocial and behavioural factors in the explanation of inequalities in adolescent health. Methods Data were obtained from the German part of the cross-sectional 'Health Behaviour in School-aged Children' Survey in 2006, with a total of 6997 respondents aged 11-15 years (response rate 86%). Socioeconomic position was measured using the Family Affluence Scale. Multistage logistic regression models were used to assess the relative importance of explanatory factors. Results Compared with adolescents from high affluent backgrounds, the ORs of fair/poor self-rated health increased to 1.53 (95% CI 1.11 to 2.12) in low affluent boys and to 2.08 (95% CI 1.62 to 2.67) in low affluent girls. In the separate analyses, material, psychosocial and behavioural factors attenuated the OR by 30-50%. Together, the three explanatory factors reduced the OR by about 80% in low affluent boys and girls. The combined analyses illustrated that material factors contributed most to Conclusions The findings show that the main explanatory approaches for adults also apply to adolescents. The direct and indirect contribution of material factors for inequalities in self-rated health was stronger than that of behavioural and psychosocial factors. Strategies for reducing health inequalities should primarily focus on improving material circumstances in lower affluent groups.