Reuters/Jason Cohn
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The CDC survey counted 1.2 million victims of rape and attempted rape that year, compared to just about 188,000 counted by the NCVS.
The cause of this disparity may be that the CDC survey asks better questions, as Slate's Emily Bazelon points out. The NCVS buries its question about sexual assault among other questions about crime, asking people if they've experienced "any rape, attempted rape or other type of sexual attack." People who have had sex against their will - if a boyfriend had sex with them while they were passed out drunk - might not think of it as "rape."
The CDC apparently accounted for this phenomenon, specifically asking people if others had sex with them when they were "drunk, high, drugged, or passed out and unable to consent." The CDC also asks if others had used physical force or threats to get them to have various kinds of sex.
Because of the stigma associated with rape, it will probably always be reported less than, say, auto theft.
But the CDC may get the most accurate count possible by using neutral language and spelling out exactly what constitutes as a sexual assault.