Background: People with limited health literacy are more likely to be socioeconomically disadvantaged and have risk factors for preventable chronic diseases. General practice is the ideal setting to address these inequalities however these patients engage less in preventive activities and experience difficulties navigating health services. This study aimed to compare primary care patients with and without sufficient health literacy in terms of their lifestyle risk factors, and explore factors associated with receiving advice and referral for these risk factors from their GPs. Methods: A mailed survey of 739 patients from 30 general practices across four Australian states was conducted in 2012. Health literacy was measured using the Health Literacy Management Scale. Patients with a mean score of <4 within any domain were defined as having insufficient health literacy. Multilevel logistic regression was used to adjust for clustering of patients within practices. Results: Patients with insufficient health literacy (n = 351; 48%) were more likely to report being overweight or obese, and less likely to exercise adequately. Having insufficient health literacy increased a patient's chance of receiving advice on diet, physical activity or weight management, and referral to and attendance at lifestyle modification programs. Not speaking English at home; being overweight or obese; and attending a small sized practice also increased patients' chances of receiving advice on these lifestyle risks. Few (5%, n = 37) of all patients reported being referred to lifestyle modification program and of those around three-quarters had insufficient health literacy. Overweight or obese patients were more likely to be referred to lifestyle modification programs and patients not in paid employment were more likely to be referred to and attend lifestyle programs. Conclusion: Patients with insufficient health literacy were more likely to report receiving advice and being referred by GPs to attend lifestyle modification. Although the number of patients referred from this sample was very low, these findings are positive in that they indicate that GPs are identifying patients with low health literacy and appropriately referring them for assistance with lifestyle modification. Future research should measure the effectiveness of these lifestyle programs for patients with low health literacy.