Web scraping involves using computer programs for automated extraction and organization of data from the Web for the purpose of further data analysis and use. It is frequently used by commercial companies, but also has become a valuable tool in epidemiological research and public health planning. In this paper, we explore ethical issues in a project that “scrapes” public websites of U.S. county jails as part of an effort to develop a comprehensive database (including individual-level jail incarcerations, court records and confidential HIV records) to enhance HIV surveillance and improve continuity of care for incarcerated populations. We argue that the well-known framework of Emanuel et al. (2000) provides only partial ethical guidance for the activities we describe, which lie at a complex intersection of public health research and public health practice. We suggest some ethical considerations from the ethics of public health practice to help fill gaps in this relatively unexplored area.