While the general link between substandard housing and poor health has received increased attention recently, there are currently no widely accepted standardized protocols to assess and remediate multiple housing-related health hazards. This paper compares several protocols that assess housing health hazards, including the Hazard Assessment and Reduction Program, the American Healthy Homes Survey, the Public Housing Assessment System, the Housing Quality Standards, the American Housing Survey, the Community Environmental Health Resource Center protocol, and the National Energy Audit Tool. The comparison shows considerable variability across the protocols, particularly in the collection of environmental samples or measurements. This may be due in part to differing end uses, as well as the fact that the intersection of housing and health issues is not clearly in the domain of either profession. Housing professionals typically focus on durability and affordability, while environmental health professionals are frequently focused on specific disease or injury vectors, not on place-based interventions. Validation studies at both the national and the international level are needed to determine how well both the hazard assessment and the resulting interventions predict health outcome. Standardizing and validating such protocols can help move beyond the existing limited categorical approaches and will help improve both substandard housing quality and public health.