Background People with unknown atrial fibrillation (AF), who are often asymptomatic, have a substantially increased risk of stroke. Although recommended in European guidelines, AF screening is not routinely performed. Screening at the time of influenza vaccination presents an ideal opportunity to detect AF in large numbers in a primary care medical setting, with an existing annual recall system for patients aged ≥65 years. Design Cross-sectional pilot study of handheld smartphone electrocardiogram (iECG) screening to identify unknown AF. Methods General practices in Sydney, Australia, were recruited during the influenza-vaccination period of April-June 2015. Practice nurses screened patients aged ≥65 years with a 30-second iECG, which has a validated algorithm for detecting AF in real time. In order to confirm the accuracy of the algorithm, two research cardiologists reviewed de-identified iECGs. In order to explore barriers and enablers, semi-structured interviews were conducted with selected nurses, practice managers and general practitioners. Results Five general practices were recruited, and 973/2476 (39%) patients attending influenza vaccination were screened. Screening took an average of 5 minutes (range 1.5-10 minutes); however, abnormal iECGs required additional time. Newly identified AF was found in 8/973 patients (0.8%). The sensitivity of the iECG automated algorithm was 95% (95% confidence interval: 83-99%) and the specificity was 99% (95% confidence interval: 98-100%). Screening by practice nurses was well accepted by practice staff. Key enablers were the confidence and competence of nurses and a 'designated champion' to lead screening at the practice. Barriers were practice specific, and mainly related to staff time and funding. Conclusions Screening with iECG during influenza vaccination by primary care nurses is feasible and well accepted by practice staff. Addressing barriers is likely to increase uptake.