Background: Reliable and timely health information is an essential foundation of public health action and health systems strengthening both nationally and internationally. A well-functioning health information system is one that ensures the production, analysis, dissemination and use of reliable and timely health information by decision-makers at deferent levels of the health system. Objective: The overall objective of this study is to assess the level of HMIS data quality, information use and the associated factors in public health facilities of Sidama Zone. Methodology: A cross sectional facility based study was conducted in Sidama Zone health facilities from February to March 2018. Quantitative data was collected using structured questionnaires and check lists and while qualitative data was collected using in-depth interview to complement the findings. Both data types were collected by trained data collectors. The quantitative data was analyzed using SPSS version 21 and descriptive and logistic regression analysis was carried out. For the qualitative part, thematic analytic method was employed to identify, analyze and report the themes that are important in relation with the study objective. Results: The overall proportion of health facilities meet acceptable level of HMIS data quality was 43.8%. HMIS specific supportive supervision, availability of adequate amount of all HMIS materials and the attitude of health workers in user friendliness of HMIS tools were found to be significantly associated with acceptable level of data quality, and their strength were AOR 1.942, 95%CI [1.084, 3.480), AOR=2.136, 95% CI [1.100, 4.147]) and AOR=3.346, 95% CI [1.538, 7.280]) respectively. The level of information use practice was found to be 58%. HMIS specific supportive supervision, perception of health workers towards the staff in using HMIS data to manage the facility and gather data to find the root cause of the problem were significantly associated with information use practice with (AOR= 3.070, 95%CI [1.206, 7.816] (AOR= 3.732, 95%CI [1.383, 10.068], (AOR= 3.782, 95%CI [1.456, 9.819] respectively. Conclusions: The overall of proportion of facilities that met the acceptable level of data quality was 43.8% ,54.2% for health center, 40% for hospitals and 36.8% for hospitals. The level of information use practice among health facilities was 58.3%, Health centers (79%), Hospitals (50%) and Health post (42%). Recommendation: To improve data quality and information use practice, the higher level should provide regular support for the health facilities. The Performance review teams of health facilities should focus on regular self-assessment. Moreover, the availability of HMIS tools should be ensured in sustainable fashion. Finally, health facilities staff should afford due consideration on evidences for facility management and to find a root cause for the problem.