Nuclear medicine is the second largest source of medical radiation exposure to the general population after computed tomography imaging. Informed decisions regarding the use of nuclear medicine procedures require a better understanding of the magnitude of radiation dose and associated health risks. However, existing model-based organ dose estimation tools rely on simplified human anatomy models or commercial programs. Therefore, we developed a publicly-available dose calculation tool based on more sophisticated human anatomy models. We calculated a comprehensive library of photon and electron specific absorbed fractions (SAF) for multiple combinations of source and target regions within a series of pediatric and adult computational human phantoms matching the International Commission on Radiological Protection (ICRP)'s reference data, combined with a Monte Carlo radiation transport code. Then, we derived a library of S values from these SAFs and the nuclear decay data from ICRP Publication 107. Finally, we created a graphical user interface, named National Cancer Institute Dosimetry System for Nuclear Medicine (NCINM), to facilitate the dosimetry process. Approximately 13 million S values were derived from 2 million SAFs computed in this work. Comprehensive comparisons were conducted at different steps of the dosimetry chain with data available in software OLINDA/EXM 1.0 and IDAC 2.1. For instance, median ratios of photon self-absorption SAFs available from OLINDA/EXM 1.0 and IDAC 2.1 to those calculated in this study were 1.3 (interquartile range = 1.1-1.6) and 1.0 (interquartile range = 0.98-1.0), respectively. SAF differences between NCINM and OLINDA/EXM 1.0 were explained by the large inter-phantom anatomical variability. Our results illustrate the importance of realistic human anatomy models for use in dosimetry software. More phantoms and radionuclides, as well as a biokinetic module, will soon be added. Applications of the NCINM program include computation of absorbed doses for use in radiation epidemiologic studies and patient dose monitoring in nuclear medicine.