The effectiveness of cognitive behaviour therapy for paediatric functional abdominal pain leaves room for improvement. We studied which factors addressed in cognitive behaviour therapy relate most strongly to the physical and psychological functioning of children with functional abdominal pain and are thus most important to target. Questionnaires were filled out by 117 children with functional abdominal pain and their parents. Multiple regression analyses showed that children’s passive coping and parental and children’s positive cognitions relate to child functioning. Negative cognitions and parental solicitous behaviour were unrelated to child functioning. Cognitive behaviour therapy for functional abdominal pain may benefit most from changing children’s passive coping and promoting positive cognitions.