Background: While microscopy (MS) evaluation of skin scrapings has a 100% positive predictive value and specificity by definition for scabies diagnosis, it has low sensitivity. Dermoscopy (DS) has not yet been widely accepted for diagnosis, and long-term clinician training is required.To evaluate the diagnostic validity of cytochrome c oxidase subunit 1 (cox1) gene nested polymerase chain reaction (PCR) as an adjunctive method for diagnosing scabies.This was a prospective, single institution study, conducted on a total of 302 skin lesions from 50 patients suspected of scabies at Kangdong Sacred Heart Hospital in Seoul, Korea. DS, MS, and cox1 nested PCR were performed on all patients.Of the 302 lesions, 145 (48.0%) were obtained at first visit and 157 (52.0%) were identified in the course of follow-up visits after treatment. For all lesions, DS and MS sensitivity levels were 55.9% (73/136) and 55.2% (75/136), respectively, with cox1 gene nested PCR considered as 100%. The results of DS and MS identification showed no difference between each other and showed significant difference from that of cox1 gene nested PCR.Nested PCR detecting cox1 may be prospectively used to comprehensively diagnose lesions of scabies in clinical practice.