Previous studies of craniofacial risk factors for obstructive sleep apnea (OSA) have been based predominantly on cephalometry. However, differences in head form (measured by the cranial index [CI]) and facial form (measured by the facial index [FI]) are considered by anthropologists to provide a basis for structural variation in craniofacial anatomy. We assessed the association of head and facial form with the apnea hypopnea index (AHI) in 364 white individuals and 165 African-Americans. Data collected included cranial and facial dimensions (using anthropometric calipers), body mass index (BMI), neck circumference, and the AHI. CI and FI differed for whites with OSA (AHI > or = 15) versus those without OSA (AHI < 5) (increased CI and decreased FI in subjects with OSA, p = 0.005 and p = 0.006, respectively). CI and FI did not differ in OSA versus non-OSA groups of African-Americans. In subjects with OSA, the CI in whites was again greater and the FI smaller than those in African-Americans (p = 0.007 and p = 0.004, for CI and FI.) We conclude that brachycephaly is associated with an increased AHI in whites but not in African-Americans. The CI may useful in phenotyping and identifying population subsets with OSA.