This national study is an effort to measure transportation costs and affordability for the major Housing and Urban Development (HUD) housing assistance programs since the transportation costs are the second largest expense of American households. This study estimates transportation costs for 76,000 address level properties from seven major HUD-designated affordable housing programs. Our transportation cost models are tailored for low-income households and account for built environmental determinants of travel, known as D variables, at the disaggregated level. We found that more than 44% of these properties in 326 U.S. metropolitan areas are unaffordable in terms of transportation costs. That could result in a waste of over $37.9 billion HUD spends annually to run these programs and subsidize housing for low-income families while some of these families spend substantial amount of their income on transportation. Our findings suggest that the provision of subsidized housing in mixed use, and transit-served neighborhoods would help low-income households to reduce their transportation costs even in auto-oriented sprawling regions. This study concludes with policy recommendations to local and federal governments and transit agencies on ways to incorporate transportation parameters to ensure true affordability for low-income residents of subsidized housing.