Providers and non-physician staff in primary care settings have reported barriers to full electronic health record (EHR) utilization. This study evaluates the effectiveness of EHR use for accurately documenting cervical cancer screening in a community healthcare setting, and proposes strategies to improve documentation. An electronic query generated data on average-risk patients aged 21-64 who had a medical visit at Fenway Health in 2012 and were overdue for a Papanicolaou (Pap) test according to the 2012 American Society for Colposcopy and Cervical Pathology guidelines. We then conducted a manual review of these records to determine the accuracy of EHR documentation. Of a total 5,279 patients, the electronic query classified 2,982 (56.5%) as up-to-date (UTD) for a Pap and 2,297 patients (43.5%) as overdue. Upon manual review, 65 (2.2%) patients thought to be UTD were actually overdue. Of those 2,297 patients classified by the query as overdue, 816 (35.5%) were reclassified as UTD due to evidence of a recent Pap in their chart that was not extractable by electronic query and 208 (9.1%) were ineligible for a Pap; only 1,272 patients (55.4%) of the 2,297 classified by the query were truly overdue. The cervical cancer screening rate indicated by electronic query was 56.5 %; after manual review, the adjusted rate was 73.6%. Overall, 1,090 patients (20.6%) were misclassified by the query. Inefficient EHR use can have serious implications for clinical practice and performance measures. Primary care practices need to develop mechanisms to capture outside medical records and create a team-based approach to facilitate accurate EHR documentation.