The wide anatomical variation of the brachial plexus and the axillary artery has been thoroughly explored in previous studies. However, there has been little information reported on the variation in the relationship between the brachial plexus and the axillary artery. The principal feature of this relationship is the passage of the axillary artery through the loop of the median nerve, which occurs in normal arteries derived from the seventh intersegmental artery. In this study, we analyzed the abnormal position and course of the axillary artery related to the brachial plexus in 607 axillae of 306 cadavers. We found 12 unusual axillary arteries that did not pass through the median loop. Eleven arteries were determined to be ninth intersegmental arteries and one as the sixth intersegmental artery. All ninth intersegmental arteries ran caudally to the brachial plexus. In six cases of this type, abnormal connections interfering with the normal arterial position were observed in the brachial plexus. In another five cases of this type, the lateral and medial cords merged and the axillary artery passed anteromedial to the plexus. The sixth intersegmental axillary artery pierced the musculocutaneous nerve which is from the unified lateral and medial cords. This study discussed the how the anomalous structure of the brachial plexus could involve the deterioration of the course of the axillary artery.