Introduction Personal risk for multiple conditions should be assessed in primary care. This study evaluated whether collection of risk factors to generate electronic health record (EHR)-linked health risk appraisal (HRA) for coronary heart disease, diabetes, breast cancer, and colorectal cancer was associated with improved patient–provider communication, risk assessment, and plans for breast cancer screening. Methods This pragmatic trial recruited adults with upcoming visits to 11 primary care practices during 2013–2014 (N=3,703). Pre-visit, intervention patients completed a risk factor and perception assessment and received an HRA; coded risk factor data were sent to the EHR. Post-visit, intervention patients reported risk perception. Pre-visit, control patients only completed the risk perception assessment; post-visit they also completed the risk factor assessment and received the HRA. No data were sent to the EHR for controls. Accuracy/improvement of self-perceived risk was assessed by comparing self-perceived to calculated risk. Results The intervention was associated with improvement of patient–provider communication of changes to improve health (78.5% vs 74.1%, AOR=1.67, 99% CI=1.07, 2.60). There was a similar trend for discussion of risk (54.1% vs 45.5%, AOR=1.34, 95% CI=0.97, 1.85). The intervention was associated with greater improvement in accuracy of self-perceived risk for diabetes (16.0% vs 12.6%, p=0.006) and colorectal cancer (27.9% vs 17.2%, p<0.001) with a similar trend for coronary heart disease and breast cancer. There were no changes in plans for breast cancer screening. Conclusions Patient-reported risk factors and EHR-linked multi-condition HRAs in primary care can modestly improve communication and promote accuracy of self-perceived risk.