This cross-sectional study aims to 1) investigate the factor structure and measurement invariance of subjective health complaints inventory in terms of gender, 2) examine the role of selfesteem, interparental conflict and gender in Czech adolescents’ subjective health complaints, and 3) examine a possible moderating effect of gender in these relationships. Czech adolescents (N = 1602, 51% girls) from an epidemiological part of the European Longitudinal Study of Pregnancy and Childhood (ELSPAC) completed questionnaires at home and a psychological sub-sample of ELSPAC (n = 343, 46% girls) completed questionnaires during individual psychological examinations in the years 2006 and 2007. The subjective health complaints inventory used in this study is a unidimensional and scalar invariant for sex. Girls reported more subjective health symptoms than boys. Self-esteem may play a protective role for the adolescents’ subjective health symptoms, especially in boys, whereas self-blame and threat in an interparental conflict may serve as a risk factor similarly for both sexes.