Three-dimensional Multi-User Virtual Environments (MUVEs) are being increasingly used in many areas, and they are becoming more and more integrated with learning and teaching. MUVEs can be used in learning and teaching to facilitate student learning and collaboration. This study identified the effects of MUVEs on collaborative learning and social presence and investigated whether these effects varied by gender. The participants were sophomore students attending a programming language course. They used a MUVE for their group meetings as part of their collaborative work. They also held voice communication. A four-section questionnaire was administered to the students who attended the meetings, in which the researchers served as facilitators. Interviews were held with randomly selected students. In addition, the group project meetings were tape-recorded, and field notes were taken for each meeting. The results showed that the MUVE enabled the group members to exchange ideas in an authentic environment, and that the file-sharing platform used as a complement to the MUVE reinforced collaborative learning. As long as technical problems are prevented, effective collaborative learning can be achieved in these environments.