Abstract Background The future of notifiable condition reporting in the United States is undergoing a transformation with the increasing development of Health Information Exchanges which support electronic data-sharing and -transfer networks and the wider adoption of electronic laboratory reporting. Communicable disease report forms originating in clinics are an important source of surveillance data for public health agencies. However, problems of poor data quality and delayed submission of reports to public health agencies are common. In addition, studies of barriers and facilitators to reporting have assumed that the primary reporter is the treating physician, although the extent to which a provider is involved in the reporting workflow is unclear. We sought to better understand the barriers to and burden of notifiable condition reporting from the perspectives of the three primary groups involved in reporting workflow: providers, clinic staff who bear the principal responsibility for reporting, and the public health workers who receive and process reports from clinics. In addition, we sought to situate these findings within the context of the future of notifiable disease reporting and the potential impacts of electronic lab and medical records on the surveillance system. Methods Seven ambulatory care clinics and 3 public health agencies that are part of a Health Information Exchange in the state of Indiana, USA, participated in the study. Data were obtained from a survey of clinic physicians (N = 29), interviews with clinic reporters (N = 11), and interviews with public health workers (N = 9). Survey data were summarized descriptively and interview transcripts underwent qualitative analysis. Results In both clinics and public health agencies, the laboratory report initiates reporting workflow. Provider involvement with reporting primarily revolves around ordering medications to treat a condition confirmed by the lab result. In clinics, reporting is typically the responsibility of clinic reporters who vary in frequency of reporting. We found an association between frequency of reporting, reporting knowledge and perceptions of reporting burden. In both clinics and public health agencies, interruptions and delays in reporting workflow are encountered due to inaccurate or missing information and impact reporting timeliness, data quality and report completeness. Both providers and clinic reporters lack clarity regarding how data submitted by their reports are used by public health agencies. It is possible that the value of reporting may be diminished when those responsible do not perceive receiving benefit in return. This may account for the low awareness of or recollection of public health communications with clinics that we observed. Despite the high likelihood that public health advisories and guidance are based, in part, on data submitted by clinics, a direct concordance may not be recognized. Conclusions Unlike most studies of notifiable condition reporting, this study included the clinic reporters who bear primary responsibility for completing and submitting reports to public health agencies. A primary barrier to this reporting is timely and easy access to data. It is possible that expanded adoption of electronic health record and laboratory reporting systems will improve access to this data and reduce reporting the burden. However, a complete reliance on automatic electronic extraction of data requires caution and necessitates continued interfacing with clinic reporters for the foreseeable future—particularly for notifiable conditions that are high-impact, uncommon, prone to false positive readings by labs, or are hard to verify. An important finding of this study is the association between frequency of reporting, reporting knowledge and perceptions of reporting burden. Increased automation could result in even lower reporting knowledge and familiarity with reporting requirements which could actually increase reporters’ perception of notifiable condition reporting as burdensome. Another finding was of uncertainty regarding how data sent to public health agencies is used or provides clinical benefit. A strong recommendation generated by these findings is that, given their central role in reporting, clinic reporters are a significant target audience for public health outreach and education that aims to alleviate perceived reporting burden and improve reporting knowledge. In particular, communicating the benefits of public health’s use of the data may reduce a perceived lack of information reciprocity between clinical and public health organizations.