Mohs micrographic surgery (MMS) is used to treat certain high-risk non-melanoma skin cancers (NMSC) due to its high cure rate. However, clinical recurrences do occur in a small number of cases. We examined specific clinical characteristics associated with NMSC recurrences following MMS. We employed a retrospective chart review of the 1467 cases of NMSC that underwent MMS at UC San Diego from January 1, 2008 through December 31, 2009. A total of 356 cases were excluded due to lack of follow-up. Five (0.45%) of 1111 cases developed recurrences of NMSC at the site of MMS. There were 741 cases of basal cell carcinomas (BCC); 3 were recurrences (0.40%). There were 366 cases of squamous cell carcinomas (SCC); 2 were recurrences (0.55%). Review of MMS histopathology of these recurrent tumors showed that there were no errors or difficulty with the processing or interpretation of the slides. Five-year recurrence rate of NMSC following MMS at our institution is below the reported average. Our retrospective chart review identified specific clinical characteristics associated with NMSC recurrence including a history of smoking, anatomical location on the cheeks, ears or nose, and a history of immunosuppression for SCCs.