Background: The delivery of effective interventions to assist patients to improve their physical activity and dietary behaviors is a challenge in the busy primary care setting. Design: Cluster RCT with practices randomized to telephone counseling intervention or usual care. Data collection took place from February 2005 to November 2007, with analysis from December 2007 to April 2008. Setting/participants: Four-hundred thirty-four adult patients with type 2 diabetes or hypertension (mean age=58.2 [SD=11.8]; 61% female; mean BMI=31.1 [SD=6.8]) from a disadvantaged community were recruited from ten primary care practices. Intervention: Twelve-month telephone counseling intervention. Main outcome measures: Physical activity and dietary intake were assessed by self-report at baseline, 4, and 12 months. Results: At 12 months, patients in both groups increased moderate-to-vigorous physical activity by a mean of 78 minutes per week (SE=10). Significant intervention effects (telephone counseling minus usual care) were observed for: calories from total fat (decrease of 1.17%; p<0.007), energy from saturated fat (decrease of 0.97%; p<0.007), vegetable intake (increase of 0.71 servings; p<0.039), fruit intake (increase of 0.30 servings; p<0.001), and grams of fiber (increase of 2.23 g; p<0.001). Conclusions: The study targeted a challenging primary care patient sample and, using a telephone-delivered intervention, demonstrated modest improvements in diet and in physical activity. Results suggest that telephone counseling is a feasible means of delivering lifestyle intervention to primary care patients with chronic conditions-patients whose need for ongoing support for lifestyle change is often beyond the capacity of primary healthcare practitioners. Trial registration: Australian Clinical Trials Registry, Australian New Zealand Clinical Trials Registry, www.anzctr.org.au/default.aspx, ACTRN012607000195459.