Although the association between homelessness and objective indicators of poor health is well-established, little research has focused on the subjective health-related quality of life of homeless and vulnerably housed (HVH) individuals. This study examined the subjective health-related quality of life of HVH individuals, using the Multiple Discrepancies Theory (MDT) Scale for Health of the Quality of Life for Homeless and Hard-to-House Individuals (QoLHHI) Inventory, and its association with self-reported functional health status, as measured by the SF-12, and self-reported physical and mental health conditions in a sample of 100 HVH individuals recruited in Vancouver, Toronto and Ottawa. Our findings indicate that physical and mental health conditions are highly prevalent among HVH individuals and that the SF-12 Physical and Mental Component Summary scores are substantially lower compared to US population norms. The MDT Health items were not statistically significantly associated with physical or mental health conditions and only showed correlations of small to moderate magnitude with the SF-12 Component Summary Scales. These findings suggest that the QoLHHI MDT Scale for Health can provide information about HVH individuals’ subjective health experiences that is different from, and can serve as a valuable complement to, health status information for use in research and evaluation studies, as well as for policy purposes to make informed decisions based on subjective health-related quality of life data from HVH individuals.