Patient preferences for medications strongly correlate with adherence; one area of interest is the choice between branded and generic drugs. Despite extensive research about brand-versus-generic drug preferences, few studies have explored severe-illness patients like those with coronary heart disease (CHD). We could not locate studies measuring preference weights of branded drugs in different classes within guideline-recommended regimens using discrete choice experiments (DCE). We aimed to explore the preference for branded medications used for secondary prevention of CHD events among patients receiving treatment at one of the largest Egyptian health insurance clinics. Patients with CHD were interviewed to choose between various therapy regimens containing brand-name and generic versions of aspirin, beta-blockers, statins, and renin–angiotensin–aldosterone system blockers (RAAS blockers). The study employed a DCE technique and followed the recommendations of the International Society of Pharmacoeconomics and Outcomes Research (ISPOR). Seventy-two percent (149) of the 208 patients questioned were dissatisfied with at least one of their generic medications. The majority of unsatisfied patients displayed brand preferences across the four medicine classes, primarily due to the notion that generics may be less effective. Patients preferred the RAAS blocker brand the most (adjusted odds ratio [AOR]: 3.14; 95% confidence interval [CI] 2.83 to 3.48), followed by beta-blockers (AOR: 2.06; 95% CI 1.88 to 2.27) and statins (AOR: 1.5; 95% CI 1.50 to 1.61). The relative importance of each class from the patient’s perspective showed the highest importance with RAAS blockers (22.2%) and beta-blockers (14.1%), while statins and aspirin had minor importance (7.8% and 6.6%, respectively). In the present study, branded drugs for secondary CHD prevention were preferred over generic alternatives. This finding has two implications for clinical practice. Firstly, physicians and pharmacists need to assure patients about the quality of generics to insure patient satisfaction and adherence to medication. Secondly, health insurance providers need to confirm the effectiveness of generics through observational studies. Despite the well-proven protective effects of aspirin and statins, they had minor importance from the patient’s perspective, highlighting the need to enhance patient knowledge. DCE was demonstrated to be a useful tool for eliciting the genuine preferences of patients treated within the setting of health insurance.