Background and Objectives: Obstructive sleep apnea syndrome (OSAS) and chronic obstructive pulmonary disease (COPD) are usually associated with multi-morbidity. The aim of this study was to retrospectively investigate the prevalence of comorbidities in a cohort of patients with OSAS and COPD-OSAS overlap syndrome (OS) patients and to explore differences between these two groups. Materials and Methods: Included were consecutive OS patients and OSAS patients who had been referred to our sleep laboratory, and were matched in terms of sex, age, BMI, and smoking history. Presence of comorbidities was recorded based on their medical history and after clinical and laboratory examination. Results: The two groups, OS patients (n = 163, AHI > 5/h and FEV1/FVC < 0.7) and OSAS patients (n = 163, AHI > 5/h, and FEV1/FVC > 0.7), did not differ in terms of apnea hypopnea index (p = 0.346), and oxygen desaturation index (p = 0.668). Compared to OSAS patients, OS patients had lower average SpO2 (p = 0.008) and higher sleep time with oxygen saturation <90% (p = 0.002) during sleep, and lower PaO2 (p < 0.001) and higher PaCO2 (p = 0.04) in wakefulness. Arterial hypertension was the most prevalent comorbidity for both OS and OSAS, followed by dyslipidemia, cardiovascular disease (CVD) and diabetes. OS was characterized by a higher prevalence of total comorbidities (median (IQR):2 (1–3) vs. 2 (1–2), p = 0.033), which was due to the higher prevalence of CVD (p = 0.016) than OSAS. No differences were observed in other comorbidities. Conclusions: In OS patients, nocturnal hypoxia and impaired gas exchange in wakefulness are more overt, while a higher burden of CVD is observed among them in comparison to sex-, age- and BMI-matched OSAS patients.