In the context of gross anatomy education, novel augmented reality (AR) systems have the potential to serve as complementary pedagogical tools and facilitate interactive, student-centered learning. However, there is a lack of AR systems that enable multiple students to engage in collaborative, team-based learning environments. This article presents the results of a pilot study in which first-year medical students (n = 16) had the opportunity to work with such a collaborative AR system during a full-day gross anatomy seminar. Student performance in an anatomy knowledge test, conducted after an extensive group learning session, increased significantly compared to a pre-test in both the experimental group working with the collaborative AR system (P < 0.01) and in the control group working with traditional anatomy atlases and three-dimensional (3D) models (P < 0.01). However, no significant differences were found between the test results of both groups. While the experienced mental effort during the collaborative learning session was considered rather high (5.13 ± 2.45 on a seven-point Likert scale), both qualitative and quantitative feedback during a survey as well as the results of a System Usability Scale (SUS) questionnaire (80.00 ± 13.90) outlined the potential of the collaborative AR system for increasing students' 3D understanding of topographic anatomy and its advantages over comparable AR systems for single-user experiences. Overall, these outcomes show that collaborative AR systems such as the one evaluated within this work stimulate interactive, student-centered learning in teams and have the potential to become an integral part of a modern, multi-modal anatomy curriculum.