This assessment is based on an institution-based cross-sectional survey conducted with the main objective of assessing the current status of HIV/AIDS and gender responses of higher education institutions in Ethiopia. Eighteen public and four private HEIs located in nine regions of the country were covered by the study. The study was conducted between October and November 2011. The HEIs covered by this assessment have organized their HIV/AIDS program at different levels. Some of the HEI have established a designated body within their formal organizational structure to coordinate the HIV/AIDS response in their respective institution. While others have assigned the program coordination responsibility to other units or individuals including the office of deans of students, public relations office, university clinic, a health science college under the university and student clubs and/or students’ council. All of the eighteen public HEIs covered by the assessment have designated a decision making body and a program management structure on gender within their formal organizational structure. However, none of the four private HEIs has gender related programs, a unit or a structure to coordinate gender related activities. In conclusion of this study, all the public and private HEIs are recommended to establish HIV/AIDS and gender coordination units with designated office spaces and facilities, full-time coordinators and other staff members to coordinate and run the two programs in all the campuses under them. All the HEIs should also allocate up to 2% of their annual budget for HIV/AIDS programs and establish AIDS fund. Recommendations are also forwarded for all the HEIs to prepare HIV/AIDS and gender policy and strategy documents and mainstream HIV/AIDS and gender in their work. The need to address the entire communities of the HEIs with well-designed HIV/AIDS and gender interventions, link the HIV/AIDS and gender programs at all levels, involve all stakeholders in the planning, implementation, monitoring and evaluations of HIV/AIDS and gender programs are also well emphasized.