Clinical research relies on enrollment of appropriate subjects. Individuals who hear about research from their clinician are more likely to participate. We developed two strategies for research subject enrollment using the EHR and its underlying data: pop-up alerts for clinicians, and patient lists for on-site research assistants. Eleven studies used clinician alerts and most referred an adequate volume of potential subjects (range 17 to 1,162; median 324). Only a small portion of these potential subjects consented to participate (range 3% to 25%; median 11%). Two of the three studies that used EHR derived patient lists and on-site research assistants reached their enrollment goals. All three principal investigators were satisfied with this approach. These results demonstrate that EHR alerts and patient lists can facilitate research subject enrollment in primary care pediatrics. Future work will identify methods to improve the clinician EHR alert when on-site enrollment by research assistants is not feasible.