Background: The various patient-, parent-, and physician-related factors that influence the choice of a particular medication for attention-deficit/hyperactivity disorder (ADHD) have been insufficiently investigated. The physician-reported reason for choice of medication was one factor assessed in this observational study on compliance with ADHD medication. Methods: This is a baseline data analysis of a multicenter, prospective, 12-month observational study in children and adolescents with ADHD. Among other factors, the physicians reason for choice of medication was captured at baseline.The two largest medication groups (non-stimulants vs. stimulants) were compared in terms of reasons for choice of medication. Correlations were explored by Pearsons correlation coefficient, Cohens Kappa, and cluster analyses. Results: 504 patients with a mean age 9.6 years were included. Non-stimulant medication was prescribed in 50.0% and stimulant medication in 49.0% of patients (1% received both). There were no significant group differences in baseline ADHD symptom scores.Reasons for choosing non-stimulants over stimulants included: “duration of action” (73.4%/28.7%), “beneficial for compliance” (60.3%/40.1%), and “patient/parent decision” (33.7%/26.3%). Reasons for choosing stimulants over non-stimulants included: “good efficacy” (93.1%/73.0%), “good tolerability” (66.4%/44.1%), and “well-priced” (38.1%/2.8%). Conclusion: The reasons for choice of medication reported by physicians differed significantly between the two medication groups. Trial Registration Number: ClinicalTrials.gov Identifier: NCT00540826.