Introduction There are clear personal, social and environmental benefits of cycling. However, safety concerns are among the frequently cited barriers to cycling. In Australia, there are no exposure-based measures of the rates of crash or 'near miss' experienced by cyclists. Design and setting A prospective cohort study over 12 months, with all data collected via web-based online data entry. Participants Two thousand adults aged 18 years and older, living in New South Wales (Australia), who usually bicycle at least once a month, will be recruited from March to November 2011. Methods In the 12 months following enrolment, cyclists will be surveyed on six occasions (weeks 8, 16, 24, 32, 40 and 48 from the week of the enrolment survey). In these survey weeks, cyclists will be asked to provide daily reports of distance travelled; time, location and duration of trips; infrastructure used; crashes, near misses and crash-related injuries. Information on crashes and injuries will also be sought for the intervening period between the last and current survey. A subsample of participants will receive bicycle trip computers to provide objective measurement of distance travelled. Discussion This study protocol describes the prospective cohort study developed to assess near misses, crashes and injuries among cyclists by time and distance travelled and by type of infrastructure used, with recruited participants entering data remotely using the internet. We expect to be able to calculate event rates according to exposure overall and for different infrastructure types and to report in-depth information about event causation.