BACKGROUND Infectious diseases can appear and spread rapidly. Timely information about disease patterns and trends allows public health agencies to quickly investigate and efficiently contain those diseases. But disease case reporting to public health has traditionally been paper-based, resulting in somewhat slow, burdensome processes. Fortunately, the expanding use of electronic health records and health information exchanges has created opportunities for more rapid, complete, and easily managed case reporting and investigation. To assess how this new service might impact the efficiency and quality of a public health agency's case investigations, we compared the timeliness of usual case investigation to that of case investigations based on case report forms that were partially pre-populated with electronic data. METHODS Between September 2013-March 2014, chlamydia disease report forms for certain clinics in Indianapolis were electronically pre-populated with clinical, lab and patient data available through the Indiana Health Information Exchange, then provided to the patient’s doctor. Doctors could then sign the form and deliver it to public health for investigation and population-level disease tracking. Methods: We utilized a novel matched case analysis of timeliness changes in receipt and processing of communicable disease report forms. Each Chlamydia cases reported with the pre-populated form were matched to cases reported in usual ways. We assessed the time from receipt of the case at the public health agency: 1) inclusion of the case into the public health surveillance system and 2) to close to case. A hierarchical random effects model was used to compare mean difference in each outcome between the target cases and the matched cases, with random intercepts for case. RESULTS Twenty-one Chlamydia cases were reported to the public health agency using the pre-populated form. Sixteen of these pre-populated form cases were matched to at least one other case, with a mean of 23 matches per case. The mean Reporting Lag for the pre-populated form cases was 2.5 days, which was 2.7 days shorter than the mean Reporting Lag for the matched controls (p = <0.001). The mean time to close a pre-populated form case was 4.7 days, which was 0.2 days shorter than time to close for the matched controls (p = 0.792). CONCLUSIONS Use of pre-populated forms significantly decreased the time it took for the local public health agency to begin documenting and closing chlamydia case investigations. Thoughtful use of electronic health data for case reporting may decrease the per-case workload of public health agencies, and improve the timeliness of information about the pattern and spread of disease.