Breathing and sleep state are tightly linked. The traditional approach to evaluation of breathing in rapid eye movement sleep has been to focus on apneas and hypopneas, and associated hypoxia or hypercapnia. However, rapid eye movement sleep breathing offers novel insights into sleep physiology and pathology, secondary to complex interactions of rapid eye movement state and cardiorespiratory biology. In this review, morphological analysis of clinical polysomnogram data to assess respiratory patterns and associations across a range of health and disease is presented. There are several relatively unique insights that may be evident by assessment of breathing during rapid eye movement sleep. These include the original discovery of rapid eye movement sleep and scoring of neonatal sleep, control of breathing in rapid eye movement sleep, rapid eye movement sleep homeostasis, sleep apnea endotyping and pharmacotherapy, rapid eye movement sleep stability, non-electroencephalogram sleep staging, influences on cataplexy, mimics of rapid eye movement behaviour disorder, a reflection of autonomic health, and insights into cardiac arrhythmogenesis. In summary, there is rich clinically actionable information beyond sleep apnea encoded in the respiratory patterns of rapid eye movement sleep.