There is a paucity of data on the impact of organ injury on long-term outcomes after a hysterectomy for benign indications. The aim of this study was to investigate fistula formation and patient-reported long-term health outcomes after organ injury at the time of a hysterectomy. This was a population-based study of 22 538 women undergoing a hysterectomy between 2000 and 2014 in Sweden. Their medical history, characteristics of their surgery, and patient-reported outcomes were retrieved from Swedish national health and quality registers. Predictors for fistula formation were investigated with logistic regression and are presented as odds ratios with a 95% CI. Fistulas were reported in 7% of women with organ injuries, compared with 0.4% of those without organ injuries (adjusted odds ratio 15.29 [9.81-23.85]). Laparotomy and postoperative infection were associated with postoperative fistulas. Most of the women reported having better health 1 year after the hysterectomy, but 7% of those with organ injuries and 24% of those with fistulas reported deteriorated health, compared with 2% of women without injuries. Organ injury at the time of hysterectomy is associated with the development of fistulas involving the female genital tract and increases the proportion of women reporting deteriorated health 1 year after surgery.