While substantial research has demonstrated the poor health status of homeless populations, the health status of vulnerably housed individuals is largely unknown. Furthermore, few longitudinal studies have assessed the impact of housing transitions on health. The health and housing in transition (HHiT) study is a prospective cohort study that aims to track the health and housing status of a representative sample of homeless and vulnerably housed single adults in three Canadian cities (Toronto, Ottawa, and Vancouver). This paper discusses the HHiT study methodological recruitment strategies and follow-up procedures, including a discussion of the limitations and challenges experienced to date. Participants (n = 1,192) were randomly selected at shelters, meal programmes, community health centres, drop-in centres, rooming houses, and single-room occupancy hotels from January to December 2009 and are being re-interviewed every 12 months for a 2-year period. At baseline, over 85% of participants reported having at least one chronic health condition, and over 50% reported being diagnosed with a mental health problem. Our findings suggest that, regardless of housing status, participants had extremely poor overall health.