Structural variations of the thoracic outlet create a unique risk for neurogenic thoracic outlet syndrome (nTOS) that is difficult to diagnose clinically. Common anatomical variations in brachial plexus (BP) branching were recently discovered in which portions of the proximal plexus pierce the anterior scalene. This results in possible impingement of BP nerves within the muscle belly and, therefore, predisposition for nTOS. We hypothesized that some cases of disputed nTOS result from these BP branching variants. We tested the association between BP piercing and nTOS symptoms, and evaluated the capability of ultrasonographic identification of patients with clinically relevant variations. Eighty-two cadaveric necks were first dissected to assess BP variation frequency. In 62.1%, C5, superior trunk, or superior + middle trunks pierced the anterior scalene. Subsequently, 22 student subjects underwent screening with detailed questionnaires, provocative tests, and BP ultrasonography. Twenty-one percent demonstrated atypical BP branching anatomy on ultrasound; of these, 50% reported symptoms consistent with nTOS, significantly higher than subjects with classic BP anatomy (14%). This group, categorized as a typical TOS, would be missed by provocative testing alone. The addition of ultrasonography to nTOS diagnosis, especially for patients with BP branching variation, would allow clinicians to visualize and identify atypical patient anatomy.