BACKGROUND: Activation of the immune system has been demonstrated in atopy and functional gastrointestinal disorders (FGIDs). Previous data from our group have suggested a connection between immune dysregulation, FGIDs and mood disorders. AIM: To investigate if these data translate to clinical practice and examine connections from the perspective of FGIDs to determine whether atopy and FGIDs are connected via mood disorders. METHODS: Evidence of irritable bowel syndrome (IBS), functional dyspepsia (FD) and constipation was sought from the medical records of 30,000 primary care records over a minimum 5 year period. The same records yielded diagnoses of four atopic conditions (asthma, eczema, allergic rhinitis/hay fever and conjunctivitis). RESULTS: Atopic conditions were found in excess among all FGID groups considered when compared with controls. In the groups with IBS alone (OR = 1.43, 1.29-1.58), FD alone (OR = 1.41, 1.26-1.58) and those with multiple FGIDs (OR = 1.92, 1.75-2.12) there was elevated prevalence of asthma compared with controls without a FGID. Across disorders the excess was generally highest among patients diagnosed with multiple FGIDs (rhinitis/hay fever OR = 3.74, 3.32-4.20; conjunctivitis OR = 3.00, 2.49-3.62) and was only partly explained by a common association between both FGIDs and atopic conditions with mood disorders, although not for every atopic/FGID combination (rhinitis/hay fever OR = 2.60, 2.29-2.96, conjunctivitis OR = 2.34, 1.90-2.87). CONCLUSIONS: Irritable bowel syndrome, functional dyspepsia and constipation share an association with atopy that is only partly explained via a common connection with mood disorders. These data have important implications for understanding both the pathophysiology of functional gastrointestinal disorders and development of new treatments.