Objective To compare factors considered by parents to those considered by adolescents making decisions about chronic disease treatments. Methods We conducted individual interviews with 15 parent–adolescent dyads in which the adolescent had either juvenile idiopathic arthritis or Crohn's disease. Questions focused on treatment decisions, with an emphasis on the factors that influenced each individual's preferences related to biologic therapies. A multidisciplinary team developed a coding structure. All interviews were coded by two people with disagreements resolved through discussion. We used content analysis and coding matrices to examine decision factors within and between parent–adolescent dyads. Results Parents and adolescents both participated in decisions about treatment with biologic therapies but considered decision factors differently. In only half of cases did parents and adolescents agree on the factor that most influenced their decision. Although their decision factors often fell into similar categories (e.g. treatment risks, quality of life), in many cases the specifics varied between adolescents and their parents. Adolescents were more likely to focus on immediate treatment effects and quality of life while parents took a longer term view of the decision. Agreement within dyads was most consistent when a special circumstance influenced the treatment decision. Conclusions Differences regarding influential decision factors exist within parent–adolescent dyads. Continued research is needed to determine the extent to which such differences are due to individual preferences or to variations in the information available to each person. Future decision support interventions will need to address parents’ and adolescents’ potentially disparate views and information needs.