The human masseter is divided into compartments by aponeuroses. So far, the qualitative and quantitative features of these compartments and their aponeuroses have been scarcely investigated. This study investigated the three-dimensional compartmentalization of the masseter muscle and tested the hypothesis that aponeurosis content varies systematically across different masseter subportions as well as between genders. The right masseter of 14 healthy participants was scanned by magnetic resonance, and the outlines of muscle and aponeuroses were segmented and rendered in three dimensions by AMIRA software. The internal architecture of the masseter muscle varied markedly across individuals, with respect to the number, shape and location of the compartments delimited by aponeuroses. Aponeuroses were widely represented inside the masseter, amounting to 7.1 ± 2.1% of its volume. The aponeurosis content varied systematically across masseter subvolumes and did not differ between genders after adjusting for body height and weight.