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The study was carried out to compare the research output of academics in science and engineering faculties in southern Nigeria using bibliometric analysis. Descriptive survey method was used for the study. Through stratified random sampling six federal universities were selected out of 13 for the study. Two hundred and ninety-one academic staff with the rank of lecturer II and above were used for the study. The research output considered in this study was counting of journal articles and supervision of postgraduate students. The study showed that University of Benin had the highest publication of all the universities but mainly in local journals. However, University of Agriculture, Abeokuta had the highest articles in international journals, followed by University of Ibadan, Ibadan. University of Ibadan was the highest in masters and Ph.D supervision followed by university of Benin. The study also showed that there is no significant difference between mean productivity of academics from different universities. However there is significant difference between mean productivity of articles published in international journals. It is then recommended the all stake-holders in research and education should create conducive working environment for researchers, through funding, providing the necessary equipment, necessary information materials by equipping the libraries. Also researchers should be sponsored to local, national and international conferences and workshops. This will expose the researchers in their field and enhance publishing within and outside Nigeria. The federal government should in collaboration with NUC establish databases as has been done in other countries. This will make it easer for studies of this type to be carried out in Nigeria.