Introduction The absenteeism of students from classrooms and clinical setting has a negative impact on their performance and prolongs the length of their studying. The aim of this study was to identify the factors influencing absenteeism among students at Harar Health Science College. Methods Institution based cross-sectional study was conducted on 313 college health science students. A self-administered pre tested questionnaire which consists of teaching (6 items), course content (4 items), learning (4 items), assessment (6 items) and social problems (3 items) was used to collect data by using Stratified random sampling method with proportionate allocation. Results 38 (31.1%) was taken the highest frequency of 4 or more days absenteeism and Pharmacy department was the leading from all other health science departments. The main reasons reported for missing lectures, clinical site and skill lab were shortage of instructors at clinical site, insufficient equipment at demonstration room, inconvenient language used by the instructors and the assessment technique used by the instructors. Conclusion the overall prevalence of absenteeism from the class room as well as hospital practice was 186 (59.4%) and 115 (36.7%) respectively.