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Background Anal SCC is a rare disease mainly treated with chemoradiation. Abdominoperineal resection (APR), once the mainstay of treatment for anal cancer, now serves a role as salvage therapy for persistent or recurrent disease after chemoradiation. In addition, clinically positive nodes are currently treated by extending the radiation field to the groin. The role of inguinal lymph node dissection in recurrent or persistent anal SCC is unclear. The aim of the study is to determine the role of inguinal lymph node dissection in the management of inguinal lymph node metastasis for anal squamous cell carcinoma (SCC). Methods Retrospective analysis of patients with anal SCC in the National Cancer Database with positive inguinal nodes undergoing salvage APR between 2004 and 2014 was performed. A comparison of overall survival between patients who underwent APR with lymph node dissection versus APR only was analyzed using Kaplan-Meier plot. Results A total of 3424 patients underwent salvage APR, with 274 (8%) having clinically positive nodes. Within the subgroup that had clinically positive nodes, 195 (71%) underwent APR, whereas 79 (29%) underwent both APR and node dissection. Kaplan-Meier analysis demonstrates no difference in overall survival in the two groups (P = 0.99). Five-year survival for both groups was similar (36% versus 42%; P = 0.987). No significant difference was found when adjusted for age, gender, and Tumor Node Metastasis staging. Conclusions Inguinal lymph node dissection does not appear to improve overall survival in patients with advanced-stage anal cancer requiring salvage APR. Proper patient selection for node dissection is essential to spare patients from additional morbid procedures.