The BIO 14.6 dystrophic hamster (DH) is a genetically determined animal model of alveolar hypoventilation (AH) that exhibits a ventilatory control pattern of compensation and then decompensation similar to that in progressive forms of muscular dystrophy and nonprogressive congenital myopathies in humans. Possible causes of AH in the DH include respiratory muscle weakness, ventilation-to-perfusion inequalities, and an inadequate drive to breathe. Histochemical and contractile abnormalities of the diaphragm, reduced lung surface area available for gas exchange, abnormal pulmonary microvascular reactivity to hypoxia, altered levels of neurochemicals, and abnormal cellular regulation of calcium are among the specific factors that may contribute to the development of AH. The potential role of hypothyroidism in the development of AH is reviewed because many hypothyroid patients exhibit AH and other ventilatory dysfunctions, hypothyroidism is present in human patients and animals with muscular dystrophy, and thyroid status is known to influence lung architecture, myocyte function, and neural activity. Additional studies linking neurohormonal signals, transcellular signal processing, and control of ventilation in the DH may help us understand the etiology of AH in human disease.