Negesa has an XYdisorder of sex development and a natural testosterone level in the male range. Under rules set by the International Association of Athletics Federations (IAAF), she had to reduce her testosterone levels in order to compete in the women's category. Facing pressure to continue her career, she underwent a gonadectomy, a procedure to remove internal testes in 2012. Negesa later said the purpose of the surgery had been misrepresented to her, having been compared to an "injection".[2][3][4] The inadequate medical aftercare and physical and mental damage resulting from the surgery effectively ended her career. She returned to the track at the 2017 Ugandan Championships but completed the 1500 metres in 5:06.18 – nearly a minute below her best and a time which ranked her as a club level runner rather than an elite athlete.[5][6]
While the IAAF denied recommending or paying for the surgery, Negesa's case fueled controversy over the treatment of athletes with differences in sex development.[4][7] In 2019, the German government granted her asylum.[8] She was one of the athletes whose cases were profiled in Phyllis Ellis's 2022 documentary film Category: Woman.[9]