OBJECTIVE: To compare fees for biopsy, treatment procedure, repair, and 2-month follow-up for nonmelanoma skin cancer (NMSC) treatments: electrodesiccation and curettage (ED&C), excision, and Mohs micrographic surgery (MMS). METHODS: A cost comparison of 936 primary NMSCs diagnosed in 1999/2000 at a University affiliated dermatology practice. Clinical data was from medical record review. 2007 Medicare Fee Schedule costs determined fees for surgical care. Pearson chi-square tests, t-tests and analysis of variance compared fee differences. Linear regression determined independent effects of tumor and treatment characteristics on fees. RESULTS: Mean fees/lesion were $463 for ED&C, $1,222 for excision, and $2,085 for MMS (p < .001). For all treatments, primary procedure costs were highest (38%, 45%, and 41%). Total repair fees were higher with MMS ($735) vs excisions ($197). Fees were higher for head and neck tumors (p < .001), H-zone tumors (p < .001), and tumors smaller than 10 mm in diameter (p = .04). Regression models predicted that the treatment fees would be $2,109 for MMS and $1,252 for excision (p < .001). Tumor size greater than 10 mm in diameter (added $128), tumors on the head and neck (added $966), and MMS (added $857 vs excision) were independently related to higher fees (p < .001). CONCLUSION: Even after adjusting for risk factors, MMS has higher fees than excision for primary NMSC. Repairs accounted for the majority of this difference. These fee comparisons provide a basis for comparative effectiveness studies of treatments for this common cancer.