Background Valve replacement surgery with mechanical or biological prostheses is associated with a risk of thromboembolism and hemorrhagic complications related to complementary anticoagulation therapy. Current American and European treatment guidelines have established recommendations for the choice of heart valve prosthesis and the corresponding optimal anticoagulation therapy. The present study focuses on the presence of the abovementioned complications as well as on determining the probability of their risk. Methods We studied a cohort of 163 patients who underwent valve replacement surgery from 2002 to 2016 with either mechanical or biological prostheses. Both groups were treated with vitamin K agonist (VKA) complementary anticoagulation therapy after hospital discharge. Anticoagulation therapy was categorized into either optimal or not optimal according to the international normalized ratio (INR) values prior to the development of complications. Patients with comorbidities and other risk factors for thrombosis and/or bleeding were excluded. Results A total of 68.7% of patients underwent valve replacement with a mechanical prosthesis, and 31.3% were subjected to valve replacement with a biological prosthesis (p ≤ 0.001). Of those who received mechanical prostheses, 72.3% were younger than 60 years, and 27.7% were older than 60 years (p ≤ 0.001). Twenty-five percent of the patients had complications during the study (p ≤ 0.001), but their incidence was not associated with age (68.3% ≤ 60 years; p = 0.59). Hemorrhagic complications were the most common, observed in 48.8% of patients, followed by thromboembolic complications, seen in 26.8% of patients; both types of complications were noted in 24.4% of patients (RR 4.229 [CI 1.122-15.933]). Of the patients with complications, 95.1% received mechanical prostheses, and 4.9% received biological prostheses (p = 0.005). Among all patients who received prostheses, 49.7% had a nonoptimal INR; of these patients, 88.9%, had mechanical prostheses and 11.1% had biological prostheses (p ≤ 0.001). Conclusions Because of the high risk of thromboembolic and hemorrhagic complications, valve prostheses should be chosen carefully, and the priority of care should include prevention and follow-up, primarily for in patients requiring anticoagulation therapy.