© 2019 The Author(s). Background: Tobacco remains a leading cause of preventable death in the U.S., responsible for more than 440,000 deaths each year. Approximately 10% of these deaths are attributable to exposure of non-smokers to secondhand smoke (SHS). Residents living in public multi-unit housing (MUH) are at excess risk for SHS exposure compared to the general population. On November 30, 2016, the U.S. Department of Housing and Urban Development (HUD) passed a rule requiring all public housing agencies to implement smoke-free housing (SFH) policies in their housing developments by July 30, 2018. Methods: As part of a larger natural experiment study, we designed a protocol to evaluate indoor SHS levels before and after policy implementation through collection of repeat indoor air samples in non-smoking apartments and common areas of select high-rise NYCHA buildings subject to the HUD SFH rule, and also from socio-demographically matched private-sector high-rise control buildings not subject to the rule. A baseline telephone survey was conducted in all selected buildings to facilitate rapid recruitment into the longitudinal study and assess smoking prevalence, behaviors, and attitudes regarding the SFH policy prior to implementation. Data collection began in early 2018 and will continue through 2021. Discussion: The baseline survey was completed by 559 NYCHA residents and 471 comparison building residents (response rates, 35, and 32%, respectively). Smoking prevalence was comparable between study arms (15.7% among NYCHA residents and 15.2% among comparison residents). The majority of residents reported supporting a building-wide smoke-free policy (63.0 and 59.9%, respectively). We enrolled 157 NYCHA and 118 comparison non-smoking households into the longitudinal air monitoring study and performed air monitoring in common areas. Follow up surveys and air monitoring in participant households occur every 6 months for 2.5 years. Capitalizing on the opportunity of this federal policy rollout, the large and diverse public housing population in NYC, and robust municipal data sources, this study offers a unique opportunity to evaluate the policy's direct impacts on SHS exposure. Methods in this protocol can inform similar SFH policy evaluations elsewhere.