Objective: Increasingly, epidemiological studies are employing computerized and highly standardized interviews, such as the Composite International Diagnostic Interview (CIDIAuto), to assess the prevalence of psychiatric illness. Recent studies conducted in specialist units have reported poor agreement between experienced clinicians’ and CIDI-Auto diagnoses. In this study we investigated the concordance rate between clinicians and the CIDI-Auto for the diagnosis of six anxiety disorders and two mood disorders, whereby the CIDI-Auto was treated as the ‘gold standard’. Method: Subjects were 262 patients who were assessed by a clinical psychologist or psychiatrist and completed the CIDI-Auto at a tertiary referral unit for anxiety and mood disorders. Agreement between the clinicians’ diagnoses and the diagnoses generated by the CIDI-Auto according to both DSM-IV and ICD-10 codes, were examined by kappa statistics. Sensitivity and specificity values were also calculated. Results: Agreement between clinicians and the CIDI-Auto (DSM-IV) ranged from poor for social phobia and posttraumatic stress disorder (κ < 0.30) to moderate for obsessive– compulsive disorder (OCD; κ = 0.52). Agreement between clinicians and the CIDI-Auto (ICD-10) ranged from poor for major depressive episode (κ = 0.25) to moderate for OCD (κ = 0.57). With the CIDI diagnosis treated as the gold standard, clinicians’ diagnoses showed low sensitivity (κ < 0.70) for all the disorders except for OCD (for ICD-10), but high specificity (κ < 0.70) for all the disorders. Conclusion: Poor agreements between experienced clinicians and the CIDI-Auto were reported for anxiety and mood disorders in the current study. A major implication is that if diagnosis alone directed treatment, then patients could receive different treatments, depending on whether the computer, or a clinician, made the diagnosis.