Polycaprolactone as a material used when constructing nanocomposite structures is sufficiently studied in terms of therapeutic effect and safety of use. However, its biocompatibility in the form of three-dimensional carrier macrochambers is still a matter of debate due to changes in the way the 3D printing is done. The study was aimed to determine biocompatibility of the diffusion chamber made of polycaprolactone after implantation in the rat femoral neurovascular bundle. The study involved mature male Wistar rats. Animals of group 1 (experimental, n = 4) underwent implantation of the polycaprolactone diffusion chamber in the femoral neurovascular bundle. Group 2 (control, n = 3) included intact rats. Macroscopic assessment revealed no abnormalities at the site of implantation and in the target organs. Tissue microscopy revealed no systemic response; the number of binucleated hepatocytes was 1.05%. The stromal–parenchymal relationship values were as follows: liver — 1/33.20, adrenal glands — 1/19.53, kidney — 1/23.65, spleen — 1/26.52. On day 40, hemogram showed the increase in lymphocyte counts by 4%, the decrease in segmented neutrophil counts by 17% and monocyte counts by 17%. These findings confirm safety of using the polycaprolactone diffusion chamber and its biocompatibility when installed in the large neurovascular bundle. However, the effects of polycaprolactone degradation products require more extensive study over the longer periods of biointegration.