Smartphones with Global Positioning System (GPS) apps offer simple and accurate tools to collect data on human mobility. However, their associated ethical challenges remain to be assessed. We used the Emanuel framework to assess the ethical concerns of using smartphone GPS to record mobility patterns of young adults in rural South Africa for a larger study on mobility and HIV risk (Sesikhona). We conducted four focus groups (FGDs) with individuals eligible for the Sesikhona study. FGD data were coded using the (...) Emanuel framework. Participants perceived use of smartphone GPS to study human mobility and HIV risk as valuable. They raised concerns about invasion of privacy and confidentiality. Also mentioned were risk/benefit ratio, informed consent and ongoing respect. Concerns expressed provided a useful evidence-base for the development of a guide to inform future participants about ethical issues arising in the use of GPS technology to track mobility and health-related issues. (shrink)