Hypoperfusion of the brainstem during head rotation may be a risk factor for the development of SIDS. On this background we established a Doppler sonographic screening programme of the basilar cerebral arteries to evaluate the dependency of blood flow on head and body position.We investigated 3840 newborns (1872 girls and 1968 boys) with a birth weight of 3399 +/- 497 g and a gestational age of 39.2 +/- 1.4 weeks. The investigations were performed in the neonatal period with an average age of 4.7 +/- 3 days. In all infants blood flow was measured in the basilar artery (BA) in supine position with the head in the midline. From the flow profile peak systolic flow velocity Vs and time average flow velocity TAV were measured. Additionally flow measurements were performed in supine and prone position with rotation of the head to the right and left side. A decrease of blood flow velocities below 50% of the value in neutral position was considered to be abnormal. Retrograde or biophasic flow profiles during rotation were considered to be pathologic. In infants with abnormal or pathologic flow during rotation of the head flow measurements in the vertebral arteries (VA) were additionally performed. Blood flow velocities in the VA were measured in supine and prone position with the head in the midline position and after rotation to the right and to the left. In neutral position unilateral vertebral hypoplasia, aplasia and normal VA were differentiated. The judgement after rotation was performed such as in the BA.In 3807 infants (99.14%) blood flow velocities during head rotation did not decrease below 50% of the value measured in neutral position. In 33 infants (0.86%) a decrease of blood flow velocities below 50% could be found during rotation. In 7 infants (0.18%) a pathologic flow could be found during head rotation. 27 of the 33 infants with abnormal and pathologic blood flow in the BA during rotation showed anatomic abnormalities of the VA. 20 of these infants (61%) had unilateral vertebral hypoplasia (11 right, 9 left side), 7 (21%) had unilateral vertebral aplasia (4 right, 3 left side). 32 of the 33 infants with abnormal flow in the BA showed a decrease of blood flow in the contralateral VA during head rotation. 9 infants had an abnormal, 19 a pathologic flow within the contralateral VA. In 4 infants the corresponding VA could not be measured during head rotation. The decrease of blood flow velocities in the BA during head rotation was caused by compression of the contralateral VA at the craniocervical junction.Blood flow within the basilar artery of healthy infants is independent of body position and rotation of the head. A decrease of the flow velocities below 50% during rotation has to be considered as an abnormality. The incidence of pathologic blood flow during head rotation with 1.8@1000 approximates the incidence of SIDS. Hypoperfusion of the brainstem during head rotation may be a risk factor of SIDS.