One significant risk factor for recurrence after Mohs surgery is misinterpretation of slides. To determine how often pathologists detected incompletely excised basal cell carcinoma (BCC) on Mohs slides and to determine risk factors for incompletely excised BCCs. This retrospective study included 1653 BCCs treated with Mohs surgery in a university hospital between 2007 and 2011. For routine quality assurance, all slides were additionally reviewed by a pathologist within 1 week of the procedure. For this study, all cases that had divergent interpretations were re-evaluated by a Mohs surgeon and a pathologist. Mixed-effects logistic regression models with Mohs surgeon effects as random effects were used to determine risk factors for incompletely excised BCC. Incompletely excised BCCs were detected in 31 cases (2%), in which defects > 20 mm in diameter were an independent risk factor (odds ratio 3.58, 95% confidence interval 1.55-8.28). Other studied variables (i.e. aggressive subtype, previously treated BCC, location on nose and > 2 Mohs stages) did not affect the risk of incompletely excised BCCs. The additional review of Mohs slides might increase accurate interpretation, especially in large BCCs.