This study aimed to examine the core issues and challenges with web-based distance education programs in Turkish higher education institutes. Formative research method, which is a qualitative research method in nature, was selected to analyze web-based distance education programs thoroughly. The study group comprised 4 higher education institutes, offering web-based distance education services in 2014-2015, located in different provinces of different geographical regions in Turkey, and with varying experiences. The research used interview transcripts from semi-structured interviews, documents (weekly reports, meeting reports, presentations, organization chart, and implementation procedures) shared by the distance education centers, and information gathered from their web sites. Primary research data were compiled from interviews with representatives of the distance education centers managing and upholding distance education services while the documents acquired from these centers were used to verify the interview findings. The study resulted in 9 core issues related to (1) program launching process, (2) legislation, (3) program structure, (4) instructional design, (5) assessment and evaluation, (6) communication and interaction, (7) support, (8) technical issues, and (9) program evaluation.