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This paper examined the level of students' participation in governance of Universities. It also investigated the level of organizational effectiveness in the universities in Nigeria. The population of the study consists of all students in Federal and State Universities in Ekiti and Ondo State of Nigeria. The sample for the study was 510 subjects consisting of 400 students and 110 University administrators. The respondents were selected using stratified random sampling technique. The instruments tagged Students' Participation in University Governance Questionnaire (SPUGQ) and Organizational Effectiveness Questionnaire [OEQ] was used to elicit relevant information from the respondents. Frequency count, percentage and t-test statistics were used to analyze the data collected. The findings revealed that students' participation in University governance was low while organization effectiveness was moderate. The result showed that there was significant difference in students' participation in governance in Federal and State Universities. Students in Federal Universities participated more in the governance than students in State Universities. Finding also revealed that there was significant difference in Organizational effectiveness of Federal and State Universities. The Organization effectiveness of Federal University is higher than the State Universities. It was recommended that stakeholders in University education should ensure that students are more involved in the governance of their institutions. Also introduction of seminars and workshops on leadership training would enhance organizational effectiveness in the Universities. DOI:10.5901/mjss.2014.v5n9p400