Most cases with cleft lip and palate (CLP) have no other obvious malformation and are termed isolated CLP. The implication is that these individuals experienced a time-specific and anatomically-localized disturbance during palatogenesis but are otherwise normal. The cranial base was studied from cephalograms in subadults with isolated CLP (n = 43) to test for alterations in size and shape. Controlling for age and gender, analyses showed no size difference, but flexure of the cranial base was significantly greater in the CLP group. Taken in conjunction with increased risks of other conditions with prenatal onsets, it appears that "isolated CLP" is a misnomer and the cleft should be viewed as an overt manifestation of a more generalized growth disturbance.