The negative health consequences of tobacco and risky alcohol consumption are compounded when used concurrently. Australian preventative health guidelines recommend that general practitioners (GPs) assess and provide evidence-based intervention. No studies, however, have examined the accuracy of GP detection of concurrent tobacco use and risky alcohol consumption or the factors associated with accurate detection. This study aimed to examine the: (i) accuracy of GP detection of concurrent tobacco and risky alcohol use compared to patient self-report; and (ii) GP and patient characteristics associated with accurate detection following a single clinical encounter. Patients attending 12 Australian general practices completed a survey assessing smoking and alcohol consumption. For each participating patient, GPs completed a checklist to indicate the presence of these risk factors. GP judgements were compared to patient self-report. Fifty-one GPs completed a health risk checklist for 1332 patients. Only 23% of patients who self-reported concurrent tobacco and risky alcohol use identified by their GP. Patients who visited their GP four to six times in the last year were most likely to have concurrent tobacco and risky alcohol use were identified. It is imperative to establish systems to increase detection of preventative health risks in general practice to enable the provision of evidence-based treatments.