BackgroundAlthough efforts had made to support Universal Primary Education policies implementation in Ethiopia, less consideration was given to the important contribution of clean and healthy school. This study aimed at assessing WaSH systems of primary second cycle schools in Bensa district, Southren Ethiopia, from January 2018-March 2018.MethodsA school based cross-sectional study was conducted employing muti-stage sampling method composed of schools, school principals and school children. Accordingly, 8 randomly selected schools & principals for in-depth study, and 422 randomly sampled students from grades 5th-8th. Data were collected by questionnaire, interview, focus group discussion and observation. For qualitative part, key informants were interviewed using semi structured questionnaire on schools WaSH facilities, utilization and management. Data were processed & analyzed using spreadsheet database developed for this survey.ResultsThe result showed all schools were unable to get water all the times and 37.5% of them got water from unprotected sources. Almost all indicated that their water supply not tested for its quality. On-site observation showed that no schools had hand washing facility near latrine. Latrine student ratios were below the limit of national standard. More than half of them observed to have unclean latrines and feces had seen on the floor. Almost all schools had no maintenance plan for their WSS facilities. The level of attention given by schools and local government for school WaSH was low. Financial capacity, inter-sector and stakeholder cooperation and harmonization were also very weak.ConclusionsThe study result revealed that school WaSH facilities and its management, and sanitation and hygiene conditions had got various shortcomings. Hence, school WaSH facilities, sanitation and hygiene conditions primarily require due attention and commitment of stakeholders to realize a healthy school environment.