Some of the issues regarding introducing new radiocompounds in nuclear medicine are the distribution patterns, delivered dose to different organs, diagnostic abilities and side effects. In this study, in order to assess the biodistribution of 64Cu-DOX-loaded microcapsules, rats were IV-injected with the microcapsules, and 1, 4, 14, and 24 h later, the activities of the targeted organs were measured (%ID/g). The accumulated activities were achieved by %ID/g curves, and S-factors were obtained by MCNP outputs. The MIRD formulation and Monte Carlo method were used to determine the absorbed dose in the target organs. The biodistribution data and PET-CT images showed that the lungs were where the majority of activity was seen. According to MIRD and MCNP, the maximum dose delivered in the lungs was 5.79E+01 mGy/MBq and 4.70E+01 mGy/MBq, respectively. Also, the effective dose was 1.2E+01 for MIRD and 8.31E+00 mSv/MBq for MCNP. These results indicate that 64Cu-DOX microcapsules can be considered a new radiocompound in pulmonary imaging, and MCNP simulation can be a reliable method for internal dosimetry.