We propose an experimental protocol, based on chemical shift magnetic resonance imaging (CSI) that improves the methods presently available for the in vivo study of the thymus in small animals. Male Balb/c mice were examined in an imager-spectrometer equipped with a 4.7 T magnet. Three groups of animals with different ages were used: the first group consisted of 3-month-old mice (n = 5), the second group of 19-month-old mice (n = 5), and the third group of 26-month-old mice (n = 4). The identification of thymic parenchyma was obtained by two (T1-weighted spin-echo and CSI water-selective) images. The T1-weighted spin-echo image provided a detailed anatomical description of the organs located in the thorax. The CSI water-selective image provided a detailed description of thymic location, shape, and dimensions. The cross-sectional area of the thymus, measured from CSI images, showed a decreasing trend with increasing age. The values of the thymus-muscle contrast-to-noise ratio were measured in both spin echo and CSI images. While the contrast between thymus and muscle was greatly improved in the young and presenescent group, the difference was not statistically significant in the senescent group. In conclusion, the proposed method allows the study of thymic modification during the passage from young to pre-senescent age and from presenescent to old age. This method could be useful in studies in which experimental manipulation or drug treatments produce changes in the dimension and fat content of this organ. The proposed protocol, based on CSI, appears to be an improved methodology for study of the thymus.