The aim of the present study was to analyze the presence levels of participants who use three-dimensional multi-user virtual environments, which present new opportunities for learning. In addition, the participants' presence levels were compared in terms of gender. Participants' presence levels were examined qualitatively through online interviews, field notes, and interviews with the participants. The sample comprised 24 students, who attended Programming Languages II course in a Computer Education and Instructional Technology Department at a large state university in Central Anatolia Region of Turkey in 2011 Spring semester. Social Presence Scale and Virtual Environment Presence Questionnaire were used as data collection instruments. Field notes and interviews were used in order to obtain qualitative data. The results revealed that participants had a medium presence level and these levels did not differ in terms of gender. Also, the environmental factors leading to the formation of presence were identified in line with participants' opinions.