Pre-existing compromise of one or both vertebral arteries is considered a contraindication to neck manipulation. Current pre-manipulative screening tests may not adequately identify individuals with such compromise. It has been proposed that using a continuous wave ultrasound device (Doppler velocimeter) may assist in identifying patients presenting with flow abnormalities. The aim of this study was to determine the validity and reliability of the use of a velocimeter in detecting altered vertebral artery blood flow. Blood flow in the atlanto-axial segment of seated healthy adult volunteers (n = 60) was examined in the neutral and end-range contralateral rotation positions. Duplex ultrasound scans were performed (n = 58) and identified 17 volunteers (29.3%) with abnormal flow according to pre-determined criteria. Three trained physiotherapists blinded to the duplex examination results used a velocimeter to examine the vertebral arteries of the volunteers. The specificity of the velocimeter examination to detect abnormal flow identified by the duplex examination was fair to good (range 0.78–0.88). However, its sensitivity was poor (range 0.25–0.38) and the inter-examiner reliability was poor (κ ranged from 0.15 to 0.26). This study suggests that the velocimeter may be neither a valid or reliable tool for the detection of abnormal blood flow in the vertebral arteries.