In infancy, prior to cranial suture and fontanel calcification, the craniofacial skeleton can be easily deformed by an externally exerted force. In this study, the relationship between the sleep position and skull morphology was investigated. A group of 81 cleft lip and/or palate infants without other systemic anomalies was first seen in the craniofacial center at approximately 1 month of age. The sleep position of each infant was recorded as supine, prone, or mixed type. The body and skull growth were longitudinally measured at 1, 3, and 6 months of age. Infants sleeping in the supine sleep position tended to have a wider head width, shorter head length, and a larger cephalic index by 6 months of age. The opposite phenomena were observed in the prone sleep group. The mixed sleep group tended to have head width, head length, and cephalic index between those of the supine sleep group and the prone sleep group. During the first 3 months of life, the sleep position could mold the skull primarily in the dimension of head width. In conclusion, the supine sleep position may promote brachycephaly and the prone sleep position dolichocephaly.