Objective: Non-cardiac chest pain is a common and persistent problem for children; yet, typically, there is no clear medical cause. To date, no behavioural and/or psychological factors have been studied to explain chest pain in a pre-school paediatric sample. We hypothesized that pre-school children with medically unexplained chest pain would have higher rates of behavioural problems compared to healthy controls. Methods: We assessed 41 pre-school children with non-cardiac chest pain and 68 age matched children with benign heart murmurs as the control group using the Child Behaviour Check List-1 1/2-5 to evaluate emotional and behavioural problems. Results: Internalizing problem scores comprising emotionally reactive, anxiety/depression, and somatic complaints were higher in children with non-cardiac chest pain than in the control group. Among the possible factors, the factor that is related to behaviour problem scores, in univariate analysis, was a significant and inverse correlation between maternal education and behaviour problem scores. Also, maternal employment status was associated with behavioural problems. Children with a housewife mother were more susceptible to having such behavioural problems. Based on multiple regression analyses, being in the non-cardiac chest pain group was found to be significantly related to internalizing problems in our total sample. Conclusions: These results suggest that pre-school children with non-cardiac chest pain may experience increased levels of certain behavioural comorbidities. Systematic behavioural screening could increase the detection of behavioural problems and improve care for this population. Future studies of non-cardiac chest pain in pre-school children should include larger samples and comprehensive diagnostic assessments as well as long-term follow-up evaluations.