Background: Health impairments in adolescents associated with divorce and loss of parental contact are frequently reported. However, other family factors more likely to promote health are less researched. We examined the impact of several family factors on self-rated health (SRH). Methods: A longitudinal cohort study of 1225 students in high school aged 11 and 13 years in 2011. The students were surveyed at onset and after 2 years with SRH as the outcome measure. We adjusted for sex, age and self-rated socioeconomic status in temporal causal analyses, and adjusted for SRH at onset in residual change analyses, applying an ordinal logistic method. Adjusted analyses with each factor and multivariable models with backward exclusion were performed. We reported the predictive associations with odds ratios and 95% confidence limits. Results: The most decisive factors predicting future positive SRH were linked to confidence in communicating with both parents about bothersome issues, and the experience of parental support with school work. Furthermore, the experience of opinions being taken seriously in the family and the absence of excessive parental expectations predicted SRH positively after 2 years. Divorce had a modest impact on SRH and was mediated by the other factors. Only the absence of contact with fathers moderated the effect that divorce experience had on SRH. We ascertained the causal relationships through residual change analyses. Conclusions: As SRH in adolescence has an impact on later health and is amendable, it is important, from a public health perspective, to preserve and improve relationships and confidence between children and both parents.