Pediatric respiratory diseases have been linked to gastroesophageal reflux disease (GERD), but evidence regarding the association and its potential mechanisms continues to accumulate, and important aspects remain to be determined. Evidence for the association in two common pediatric respiratory disorders - infantile apnea and asthma in older children - and difficult clinical issues associated with the diagnosis and treatment of these two disorders are reviewed. The provocative embryological and physiological connections between the upper gastrointestinal tract and the respiratory tract, and recent understanding of the compensatory anatomy and physiology that protect the normal individual from respiratory manifestations of GERD are also explored. Dysfunctions of these protections likely underlie the pathophysiology of these disorders.