Background: Mohs' micrographic surgery is a suitable treatment and frozen section (FS) examination is the "gold standard" of surgical margins in tumoral skins. This study compared the diagnostic accuracy between the Tzanck smear test (TST) and frozen section (FS) examination for margin control in surgery for basal cell carcinoma (BCC). Methods: Fifty-nine patients with basal cell carcinoma (BCC) were included. The tumor was excised and the Tzanck smear test (TST) was taken for Papanicolaou staining (Pap staining) and reconfirmation of tumoral cells. Then a dermatologist took margins of tumoral mass. TST was taken from the margins and sent to the dermatopathologist for Pap staining. After dying, each marked fragment was sectioned separately with cryostat. Finally, diagnostic accuracy of TST compared with FS examination was analyzed. Results: The sensitivity and specificity of TST for the evaluation of margin were 0.28 and 0.95; whereas positive and negative predictive values were 0.54 and 0.85, respectively. Positive and negative likelihood values were 5.36 and 0.76, respectively. Diagnostic accuracy was 0.82. The kappa coefficient of agreement between the two methods was 0.28 (P < 0.001). Conclusions: Positive likelihood value and specificity of TST for the evaluation of margin were high; therefore, TST can be suitable in the diagnosis of BCC, but due to low sensitivity and kappa coefficient, TST alone cannot be a suitable alternative method compared to the FS examination for margin control in BCC.