Recruitment of participants for research is often difficult in primary care, especially children and adolescents. Poor recruitment often leads to extension or discontinuation of randomized controlled trials involving patients. This study describes the impact of media recruitment compared to recruitment via general practitioners (GPs) on characteristics of 152 children aged 7–17 years with functional abdominal pain (FAP) and irritable bowel syndrome. Demographics, clinical and psychosocial characteristics were compared. No clinically relevant differences were found, except for longer pain symptom duration and more diagnoses of FAP in children recruited via media compared to children recruited by their GP. Our results suggest that recruitment via media is effective to recruit children in primary care without inducing relevant baseline characteristic differences and this might decrease research recruitment load for GPs. Subgroup analyses on recruitment method are recommended because recruitment strategy might induce differences in unknown baseline characteristics between groups.