Because habitat loss is the main cause of extinction, where and how much society chooses to protect is vital for saving species. The United States is well positioned economically and politically to pursue habitat conservation should it be a societal goal. We assessed the US protected area portfolio with respect to biodiversity in the country. New synthesis maps for terrestrial vertebrates, freshwater fish, and trees permit comparison with protected areas to identify priorities for future conservation investment. Although the total area protected is substantial, its geographic configuration is nearly the opposite of patterns of endemism within the country. Most protected lands are in the West, whereas the vulnerable species are largely in the Southeast. Private land protections are significant, but they are not concentrated where the priorities are. To adequately protect the nation's unique biodiversity, we recommend specific areas deserving additional protection, some of them including public lands, but many others requiring private investment.