Incomplete excision of basal cell carcinomas (BCCs) may be followed by recurrence of the tumor. In order to detect risk factors for incomplete excision of BCCs we performed a cross-sectional study of 1278 patients who underwent a primary excision of BCCs, during a four-year period, within an ambulatory and hospital plastic surgery department setting. Incomplete excision occurred in 159 of 1478 primary excisions of BCCs (10.8%) and was significantly associated with location of the tumors in the eyelids (OR 3.64, 95% Cl 1.96-6.71), ears (OR 2.51, 95% Cl 1.25-4.94), naso-labial folds (OR 2.26, 95% Cl 0.99-5.04) and nose (OR 1.88, 95% Cl 1.30-2.71). There was an inverse association with location of the tumors in the upper limbs (OR 0.44 95% Cl 0.21-0.90), back (OR 0.12, 95% Cl 0.02-0.48) or chest (OR 0.09, 95% Cl 0.00-0.57). Baso-squamous differentiation was associated with incomplete excision of BCCs (p = 0.03). No association was observed between incomplete excision of BCCs and gender, age, setting of the operation (ambulatory vs. hospital), clinical appearance of the lesion (suspected BCCs vs. other diagnoses) or diameter of the lesions. In conclusion, incomplete excision of BCCs was associated with location of the tumors in the eyelids, ears, naso-labial folds and nose. We recommend that in patients with BCCs located in these sites, surgeons should commence particular surgical measures to avoid inadequate excisions of the tumors.