Introduction A large population suffers from obstructive sleep apnea (OSA). Most of these individuals (almost 90%) are either unrecognized or untreated OSA. These patients are at increased risk of cardiovascular diseases. Aim The aim of this study was to assess the prognostic value of Pentraxin 3 (PTX3) in OSA compared with the clinically relevant biological markers (HbA1c, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), uric acid, and fibrinogen) and to evaluate the relationship between PTX3 levels and risk of cardiovascular diseases. Patients and methods This research used a cross-sectional design and enrolled 100 participants with suspected OSA. All the participants underwent a full clinical history, a STOP-Bang questionnaire, and a polysomnography (PSG) study, and the serum biomarkers were also analyzed. Results The apnea-hypopnea index (AHI) from PSG was used to measure the OSA severity, and the individuals were distributed into three groups accordingly. Our findings showed that there was a significant difference in Pentraxin 3 and fibrinogen levels between patients with mild or moderate OSA and those with severe OSA. Pentraxin 3, at a cutoff point of greater than 4.25 ng/ml, had the highest prognostic accuracy in OSA (96%), with an AUC of 0.96. Regression analysis revealed that Pentraxin 3, with a cutoff point greater than 4.25, and CRP were significant predictors of cardiovascular disease in individuals with OSA. Furthermore, Pentraxin 3 (with a cutoff point of greater than 4.25 ng/ml) and fibrinogen were significant predictors of pulmonary embolism in patients with OSA. Conclusion Serum PTX3 was higher in patients with severe OSA than in those with mild- to moderate OSA. Furthermore, we found that OSA severity as indicated by the AHI was significantly correlated with serum PTX3. PTX3 and CRP are useful markers of cardiovascular risk in OSA.