<p>Earlier forms of distance education were characterized by minimal social interaction like correspondence, television, video and radio. However, the World Wide Web (WWW) and online learning introduced the opportunity for much more social interaction, particularly among learners, and this has been further made possible through social media in Web 2.0. The increased availability of collaborative tools in Web 2.0 has made it possible to have online collaborative learning realized in Higher Learning Institutions (HLIs). However, learners can perceive the online collaborative learning process as challenging and they fail to utilize these collaborative tools effectively. Although a number of challenges have been mentioned in the literature, considerable diversity exists among countries due to diversity in infrastructure support for e-learning and learners’ background. This motivated this study to investigate components of online collaborative learning perceived as challenging by learners in HLIs in Kenya. Using a questionnaire, a survey was conducted in two public universities and two private universities to identify students’ perceived challenges in an online collaborative learning environment. Through purposive sampling the questionnaire was distributed to 210 students using e-mail and 183 students responded. Based on descriptive analysis the following five major challenges were rated as high: lack of feedback from instructors, lack of feedback from peers, lack of time to participate, slow internet connectivity, and low or no participation of other group members. There was also a relationship between the university type (private or public) with the perceived challenges which included: lack of feedback from the instructor (p=0.046) and work load not shared equally among group members (p=0.000). Apart from slow internet connectivity the rest of the challenges were in line with the observed challenges in the literature.These key challenges identified in this study should provide insight to educators on the areas of collaborative learning that should be improved in order to provide access to quality education that supports effective online collaborative learning in HLIs in Kenya.</p>