Surgical treatment of complicated anal fistulas remains one of the most difficult issues of coloproctology. In this study we used a modification of Fistula Laser Closure procedure in complex treatment of patients with anal fistulas. The purpose of our study was to assess the short-term and remote results of applying the modified FiLaC procedure in patients with complex anal fistulas and compare these results with conventional fistulectomy. The patients with complex transsphincteric and extrasphincteric anal fistulas were prospectively divided into FiLaC and conventional fistulectomy groups. The operative duration was longer, by 31% (p<0.05), in the FiLaC group compared to the control group. The healing of fistulas was faster by 42% (p<0.05)in the FiLaC group (7.3 ± 0.5 weeks versus 12.6 ± 0.7 weeks). The Wexner Incontinence scale scores were significantly lower (p<0.05) in the FiLaC group. The recurrence of rectal fistula after the surgery was observed in 37.2% in the control group versus 17.5% in the FiLaC group (p<0.05) (median follow up period — 13 months). The pressure parameters of the anal sphincter were significantly higher (p<0.05) in the longterm follow-up period in patients of the FiLaC group and continence was maintained in 92.5% of the FiLaC group. Thus, the study has shown that the modified FiLaC procedure accelerates the healing time of the fistula by 42% (p<0.05), reduces the number of fistula recurrences from 37.2% to 17.5% (p<0.05), and has minimal negative effects on anal continence.