The Bureau of Justice Statistics has this report on "Sexual Violence Reported by Correctional Authorities, 2005." The data are compiled pursuant to the Prison Rape Elimination Act of 2003. There were 6241 allegations made to authorities in 2005.
All categories of crime are underreported to some degree, but this one is probably exceptionally so, as the report recognizes: "Administrative records alone cannot provide reliable estimates of sexual violence. Due to fear of reprisal from perpetrators, a code of silence among inmates, personal embarrassment, and lack of trust in staff, victims are often reluctant to report incidents to correctional authorities." BJS is working on a survey method to supplement the reported-to-authorities method. It will be interesting to see how much the two measures diverge.
For those who think that sexual violence in prison a laughing matter, it is not. Besides the obvious point that one is not sentenced to be raped in a civilized society, prison rape can spread infectious disease and has been attributed as a cause of more violent crime upon release--including the infamous James Byrd dragging case. One cannot help also to wonder if child sex predators, who don't do so well in the joint, are more highly incentivized to kill their victims due to their experiences in prison.
I would think, also, that the incidence of rape in prison is an opportunity to incarcerate dangerous felons for even longer periods. If a violent felon rapes while in prison, he should be charged and given a consecutive sentence. The death penalty, in my view, ought to be available to any prisoner who rapes a guard.