The purpose of this work is to study phenotypic craniofacial traits of unaffected parents of individuals with nonsyndromic cleft lip with or without palate (NSCL/P). In order to evaluate these craniofacial traits, three dimensional photographs were obtained and landmarked to compare the sample of unaffected parents with a control sample. The sample was comprised of 40 unaffected fathers, 25 control males, 84 unaffected mothers, and 34 control females. Twenty-four three-dimensional landmarks were exported for analysis for each subject. For the purposes of this study, nine euclidean distances were subjected to a discriminant function analysis to evaluate their ability to discriminate between an unaffected parent and a control. In both the male and female analysis, certain craniofacial measurements correctly and significantly discriminated between unaffected parents and controls. It appears that certain facial traits are subclinical markers for enhanced genetic susceptibility to nonsyndromic cleft lip with or without palate.