Obstructive sleep apnea (OSA) and hypothyroidism are relatively common disorders that have similar clinical features and are thought to be causally linked. We sought to determine the prevalence of previously unrecognized hypothyroidism in a series of patients evaluated for OSA and whether an association between hypothyroidism and OSA was present. Chart review was used to obtain information on thyroid function status, polysomnography results, levothyroxine use, and clinical signs and symptoms in 336 consecutive adult patients who underwent polysomnography for suspected OSA. In addition, levothyroxine use was determined in age- and sex-matched control subjects for the purposes of a case-control study. Among the patients without prior history of hypothyroidism who underwent polysomnography and thyroid function testing, four new cases or 1.41% (95% CI 0.04–2.78) were found to have subclinical hypothyroidism. Our findings do not support routine thyroid screening by specialists in patients referred for polysomnography. The odds ratio of the association of prior history of hypothyroidism to OSA was 1.47 (95% CI 0.8–2.8). Limitations in study design may have limited our ability to detect a statistically significant association between OSA and hypothyroidism.