van der Woude syndrome (VWS) is a congenital malformation characterized by lower lip pits with or without cleft lip or cleft palate. It is an autosomal-dominant inherited disorder with variable expression in clinical manifestation. Microdeletion in chromosome bands 1q32-q41 and recently identified mutation in interferon regulatory factor 6 gene (IRF6) have been reported to cause VWS. We report a case of VWS with lower lip pits as its main clinical manifestation without associated cleft in lip or palate. No mutation or deletion was found in the IRF6 gene or promoter site, indicating the heterogeneity of this defect.