According to an article from Contemporary Sexuality, it is very difficult to accurate count the population of transgendered people in the U.S., in general. However, the author did provide an estimate:

"The size of the transgendered population is difficult to estimate, much less define; recent published statistics put the numbers at anywhere from 2 percent to 6 percent of the general U.S. population. Harder still is gathering figures on transgender inmates from corrections authorities. The Justice Department reports there were, in 1999, 2,026,596 Americans in all jails and prisons; and there are 690 prisoners per 100,000 U.S. residents, according to The Sentencing Project, a nonprofit prison research and advocacy organization in Washington. These numbers suggest, however unreliably, that transgendered inmates number in the thousands, or even tens of thousands."

Richard D. Trans behind bars: Officials, activists struggle with options. Contemporary Sexuality [serial online]. September 2000;34(9):1. Available from: MasterFILE Premier, Ipswich, MA.