According to Queer Injustice:
The statistics don't get any better, either. One study of six male prisons in California found that 67% of the respondents who identified as LGBT* reported having been sexually assaulted by another inmate during their imprisonment. That rate is fifteen times higher than the rest of the prison population. To add on to that, some transgender women reported being subjected to strip searches and frisks four to five times a day.
Queer Injustice went on to say that:
The problem for the LGBT* community in prison is not just that they are the most targeted for harassment and sexual abuse, but that prisons are not equipped to handle the discrimination, either. If prisons do anything at all to address this discrimination, they end up accusing the victim of being the aggressor, sometimes insisting that the act must be consensual, because they are homosexual. If the prisons do separate the victimized from the general population, it isn't into a healthier population. They are usually put in protective custody, the problem with this however, is that protective and disciplinary custody are often the same, which means that even though prisoners are supposed to be in 'protective' custody, they are often held with the most violent inmates in highly restrictive and isolated settings and sometimes in more or less permanent lockdown or solitary confinement. This confinement prevents them from participating in drug treatment (like Hormone Replacement Therapy, or HRT), education or job-training programs, from having contact with other prisoners or outside visitors or from enjoying privileges such as the right to watch, television, listen to the radio, or even to leave their cells.
It's very simple. People should have the right to be housed, not by their biological sex, but by the gender they identify as. As it stands, a transwoman trying to gain entry into a female prison would have to give up their physical ability to have children and have their reproductive organs removed. All of that only comes if the individual is approved by a strenuous process of doctors appointments, psychological evaluations and drug tests.
People have the right not to be raped in prison, and that's true no matter the person's sexual orientation, gender identity, or whatever else. The prison guards and personnel must be screened and closely monitored. Prison's shouldn't be places of perpetuated crimes, they should be places of rehabilitation. All prison guards and personnel need to be trained and taught how to treat people in the LGBT* community and how to handle situations where they are being abused or mistreated. Transgender people should be housed with their gender identity and not their sex and gays and lesbians should be housed separately, but not isolated unfairly.
If the prison system can offer people television, radio, training and education, then it should equally offer things necessary for a person to transition, such as therapy and hormones.
Transgender Law Center
Human Rights Watch