The Department of Clinical Epidemiology (DCE) of the University of the Philippines Manila is the only higher education institution in the Philippines offering graduate studies in clinical epidemiology. The Master of Science Epidemiology (Clinical Epidemiology) was first offered in 1992, while the Diploma in Epidemiology (Clinical Epidemiology) was offered in 1998. While the courses of the programs are continuously updated based on students' feedback and advances on topics covered, the point of view of the students and alumni on the program as a whole has not been done. This study aimed to determine 1) self-reported current positions and affiliations, work areas where clinical epidemiology (CE) training is useful, and skills gained from CE training; 2) research studies completed and deemed by respondents to have considerable impact; and 3) strengths, weaknesses, and areas of improvement of the DCE graduate programs. This is an online survey of students and alumni of the DCE graduate programs. We sent email invites to all 287 students and alumni. We collected data on their profession, institutional affiliations, positions, skills gained from their training, areas of clinical epidemiology applications, important research involvement, reasons for recommending or not recommending the programs, and how the graduate programs can be improved. Responses were summarized by frequencies and percentages. An analyst performed qualitative content analysis (QCA) to generate strengths and weaknesses of the program. We validated the results of the QCA through 1) presentation to the research team, 2) sending the survey report to study participants and other students and alumni for feedback, and 3) presentation to the DCE faculty and staff. We received 159 responses (55.4% of the total study population)-145 (91.2%) were from the MSc program and 11 (6.9%) were from the Diploma program. Majority of the respondents were physicians (93.7%), had hospital affiliations (81.8%), and were affiliated with the academe (61%). Majority of the respondents used clinical epidemiology in their research endeavors (87.4%), clinical practice (85.5%), and teaching (78%). Majority (93.1%) would recommend the program they have taken. Eleven (6.9%) respondents were hesitant due to the possible mismatch with the students' career path, challenging thesis work, and potential conflicting personal responsibilities. Several strengths of the programs were identified, including excellent and well-implemented programs, supportive faculty and staff, and relevant course work. While completing the course work had not been a problem in general, the main challenge encountered by students is the completion of their thesis, leading to a low graduation rate in the Master of Science program. Suggestions to improve the Master of Science and Diploma programs include 1) Improvement in program implementation, including thesis policies and support, smoother transition from Diploma to MSc Program and vice-versa, and implementation of a blended learning platform; 2) Curricular improvements such as wider choices for electives and tracking towards specialty areas; 3) Innovations in conduct of courses; and 4) Personnel and infrastructure development. This survey reiterated the importance of clinical epidemiology graduate programs in research capacity building of health care professionals. Students and alumni occupied diverse positions in academic, research, clinical, and pharmaceutical setting, and majority accomplished research studies with considerable impact. A major challenge leading to a low graduation rate in the Master of Science program is the completion of thesis work. The survey identified several initiatives towards continuous quality improvement of clinical epidemiology programs, including improvement of thesis policies and support, updating the curriculum content and materials, increasing allotment of hours for hands-on activities, exploring possibilities of offering electives in partnership with other institutions, offering a blended learning platform, maintaining an efficient administrative support for students, and continuing education for alumni. Strong institutional support for personnel and infrastructure development is essential for these initiatives to succeed.