Background: Running is associated with desirable lifestyle changes. Therefore several initiatives have been undertaken to promote running. Exact data on the health effects as a result of participating in a short-term running promotion program, however, is scarce. One important reason for dropout from a running program is a running-related injury (RRI). The incidence of RRIs is high, especially in novice runners. Several studies examined potential risk factors for RRIs, however, due to the often underpowered studies it is not possible to reveal the complex mechanism leading to an RRI yet. The primary objectives are to determine short- and long-term health effects of a nationwide "Start to Run" program and to identify determinants for RRIs in novice runners. Secondary objectives include examining reasons and determinants for dropout, medical consumption and economical consequences of RRIs as a result of a running promotion program. Methods/design: The NLstart2run study is a multi-center prospective cohort study with a follow-up at 6, 12, 24 and 52 weeks. All participants that sign up for the Start to Run program in 2013, which is offered by the Dutch Athletics Federation, will be asked to participate in the study. During the running program a digital running log will be completed by the participants every week to administer exposure and running related pain. After the running program the log will be completed every second week. An RRI is defined as any musculoskeletal ailment of the lower extremity or back that the participant attributed to running and hampers running ability for at least one week. Discussion: The NLstart2run study will provide insight into the short- and long-term health effects as a result of a short-term running promotion program. Reasons and determinants for dropout from a running promotion program will be examined as well. The study will result in several leads for future RRI prevention and as a result minimize dropout due to injury. This information may increase the effectiveness of future running promotion programs and will thereby contribute positively to public health.