In light of the current shifts in medical education from traditional lectures to more active teaching modalities, a peer-teaching program was introduced to a compulsory, second-year neuroanatomy course. A cross-sectional survey of 527 medical students in the six-year medical program of the National and Kapodistrian University of Athens was administered. The primary aim of the survey, which was distributed to second- through sixth-year medical students, who had completed the neuroanatomy course, was to assess student perception of peer teachers (PTs). Across the five years assessed, students increasingly acknowledged the contribution of PTs to their learning (P < 0.001). Attributes of PTs (e.g., contribution to learning, motivation, effective usage of material, and team environment) were significantly related to the student's opinion of the importance of laboratory activities (P < 0.001). Students who received "average" final grades scored the importance of laboratory exercises, and by inference PTs, significantly lower than students who received "excellent" final grades (P < 0.05). The amount of training that PTs had received was also significantly related to student perceptions of a PT's contribution. Better trained PTs were associated with significantly higher scores regarding learning, motivation, and positive environment compared to less trained PTs (P < 0.05). The results of the present study show that peer-teaching was well received by students attending the neuroanatomy course. While the results express the evolution of the program across the years, the findings also show that learners believed that PTs and the laboratory program contributed significantly to their understanding of neuroanatomy.