Application of genetic engineering in agricultural production remains a controversial agenda in the international and national levels. The purpose of this study is to generate information on level of awareness and attitude of social and applied science lecturers towards Genetically Modified (GM) foods. The information will contribute to the national debate and decision-making processes regarding use of GM foods in Kenya. A total of 220 lecturers were randomly interviewed to a cross-sectional survey that was conducted by use of a pre-tested semi-structured questionnaire. The study was conducted at the University of Nairobi’s College of Agriculture and Veterinary Sciences (CAVS) and College of Humanities and Social Sciences (CHSS). An association was established between the levels of knowledge and the scientific background of a college. A higher proportion (48.1%) of the lecturers had a positive attitude on application of genetic engineering to solve some of the agricultural production challenges but on the other hand, they were very skeptical to consume GM foods. It was found out that the level of knowledge influenced attitudes of lecturers. Those with low knowledge are more negative to application of genetic engineering, while the ones with more knowledge are less negative on application of this technology. The main concerns of GM foods are food safety, human and environmental health. Recommendations were the government should create awareness on the biosafety legal framework; extensive research on GMOs should be done to address concerns of food safety, human and environment health; similar studies should be done in other universities and to the public, research findings from the ongoing trials on GM crops should be shared with all stakeholders and people should be educated on the pros and cons of GMOs to be able to contribute to the GMOs debate and also make informed choices.