Background Fournier's Gangrene (FG) is a low incidence disease associated with high morbidity and mortality. The main objective of this study is to analyze the impact of derivative colostomy on the course of FG. The secondary objective is to assess if derivative colostomy recommendation should be immediate or delayed in the natural history of the disease, in order to diminish morbidity Methods A prospective cohort of patients presenting FG and treated in a single center from 1996 to 2015 was studied. Patients who underwent derivative colostomy (DC) were compared to those without derivative colostomy (no-DC). Patients included in the DC group were subdivided into those who underwent colostomy at the first surgery (immediate colostomy) and those with delayed colostomy. Results Forty-six patients with FG were included. DC group included 22 patients (48%) and no-DC group, 24 patients (52%). No differences were observed in hospital stay in, numbers of interventions or mortality rates. Patients with anorectal abscess tended to receive more derivative colostomy (55% vs 8%, p = 0.006). The subgroup with immediate colostomy had a higher mortality rate compared to the subgroup with deferred colostomy, not being statistically significant (37% vs. 14%, p = 0,11). Conclusions Derivative colostomy in FG improves local disease control, but when performed in the first surgery, it is associated with higher mortality.