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The Healthy High School (HHS) intervention was developed to promote well-being among first-year high school students (~16 years of age) in Denmark by targeting stress, physical activity, meal habits, sleep, and sense of community. Thirty-one schools were randomly allocated to intervention (16 schools) or control (15 schools) groups in a cluster-randomized controlled trial. The purpose of this short communication was to compare characteristics of students and schools between 1) schools accepting to participate in the HHS study and non-participating schools using national survey data and 2) intervention and control schools using HHS baseline data. We included cross-sectional data from the Danish National Youth Study 2014 on 119 schools and 22,935 first-year students to characterize participating schools and students. At baseline (August 2016), students (n = 4577; 88.0%) and principals (n = 29; 96.7%) completed online questionnaires. Compared to non-participating schools, fewer HHS schools perceived their school as being popular and offered weekly sport activities outside school hours. More HHS schools had teachers engaged in health promotion activities and focused on stress prevention. The characteristics of HHS students did not differ markedly from non-participating high school students. There were no socio-demographic, outcome or contextual differences between the study arms. To ensure successful recruitment of schools it is important that the intervention meets the need of the schools and that the advantages of participation are explicit. This underlines the need for a thorough needs assessment prior to intervention development, co-creation of intervention activities with school staff, and a well-planned recruitment strategy.