Breathing concerns in athletes are common and can be due to a wide variety of pathology. The most common etiologies are exercise-induced bronchoconstriction (EIB) and paradoxic vocal fold movement disorder (PVFMD). Although some patients may have both, PVFMD is often misdiagnosed as EIB, which can lead to unnecessary treatment. The history and physical exam are important to rule out life threatening pulmonary and cardiac causes as well as common conditions such as gastroesophageal reflux disease, sinusitis, and allergic etiologies. The history and physical exam have been shown to be not as vital in diagnosing EIB and PVFMD. Improvement in diagnostic testing with office base spirometry, bronchoprovocation testing, eucapnic voluntary hyperpnea (EVH) and video laryngoscopy are essential in properly diagnosing these conditions. Accurate diagnosis leads to proper management, which is essential to avoid unnecessary testing and save healthcare costs. Also important to the physician treating dyspnea in athletes is knowing regulations on medications, drug testing, and proper documentation needed for certain organizations. The differential diagnosis of dyspnea is broad and is not limited to EIB and PVFMD. Ruling out life threatening cardiac and pulmonary causes with a proper history, physical, and appropriate testing is essential. The purpose of this review is to highlight recent literature on the diagnosis and management of EIB and PVFMD as well as discuss other potential causes for dyspnea in the athlete.