Carpal tunnel syndrome is associated with increased intracarpal canal pressure. The effect of tendon loading on intracarpal canal pressures is documented in biomechanical studies. Palmaris longus loading in wrist extension induces the greatest absolute increase in intracarpal canal pressure. Despite this fact, the palmaris longus is not yet a proven independent risk factor for the development of carpal tunnel syndrome. The purpose of this prospective clinical study was to assess and quantify the association between the presence of a palmaris longus tendon and carpal tunnel syndrome. Thirty-six carpal tunnel subjects with bilateral disease were compared with 36 controls. Each subject was clinically examined for the presence of the palmaris longus tendon. The prevalence of palmaris longus agenesis was significantly lower in the carpal tunnel group. The palmaris longus tendon is a strong independent risk factor for carpal tunnel syndrome.