Variations in the cerebrovascular tree can increase surgical or interventional morbidity. To date, only scant comments are to be found in the literature regarding intraluminal variations of the basilar artery. To further elucidate such anatomy, a cadaveric study was performed. One hundred and fifty human brains were evaluated for the present study. The basilar artery was identified in each and sectioned longitudinally to observe for the presence of intraluminal septa. One specimen (0.67%) was identified that harbored an intraluminal septum of the basilar artery. This wall was within the proximal basilar artery and measured 3 mm by 1.5 mm. No specimen was found to have other anomalies of the basilar artery and in the single specimen with an intraluminal septum no signs of intracranial pathology were seen. Although seemingly rare, septation of the basilar artery can be found. Knowledge of such an intraluminal vascular variation may be important during invasive and minimally invasive procedures.