In 1993, an increase was observed in the spatial IQ scores of the volunteers who listened to Mozart's sonata K448 for 10 min, and this phenomenon entered the literature as the “Mozart effect.” Other studies have shown that this effect is particularly evident in spatial skill tests. A large body of research has provided evidence that spatial ability is associated with success in learning anatomy. In this study, Kastamonu University Faculty of Medicine students were divided into two groups during 16‐h practical training spanning 30 days. While one of the groups listened to Mozart's K448 sonata as the background music in all lessons, the control group attended the lessons in their standard form. At the end of each lesson, all students solved a modified mental rotation test including questions involving anatomical structures. Before starting the study, after the first laboratory class, on the 15th and 30th day of the study, blood samples were taken from the participants, and plasma brain‐derived neurotrophic factor (BDNF) levels were determined. The effect of time on mental rotation score and plasma BDNF level was significant (p < 0.001 for both). The effect of group was also significant (p < 0.001 for both). Pairwise comparisons showed significance in the fifth, sixth, seventh, and eighth mental rotation test (p < 0.001, p = 0.041, p < 0.001, p < 0.001, respectively) and in the third (Day 15) and fourth (Day 30) BDNF measurement (p < 0.001 for both). Our findings may indicate that specific background music may be useful for anatomy teaching.