To develop a method for estimating doses to primarily exposed organs in pediatric CT by taking into account patient size and automatic tube current modulation (ATCM). A Monte Carlo CT dosimetry software package, which creates patient-specific voxelized phantoms, accurately simulates CT exposures, and generates dose images depicting the energy imparted on the exposed volume, was used. Routine head, thorax, and abdomen/pelvis CT examinations in 92 pediatric patients, ranging from 1-month to 14-yr-old (49 boys and 43 girls), were simulated on a 64-slice CT scanner. Two sets of simulations were performed in each patient using (i) a fixed tube current (FTC) value over the entire examination length and (ii) the ATCM profile extracted from the DICOM header of the reconstructed images. Normalized to CTDIvol organ dose was derived for all primary irradiated radiosensitive organs. Normalized dose data were correlated to patient's water equivalent diameter using log-transformed linear regression analysis. The maximum percent difference in normalized organ dose between FTC and ATCM acquisitions was 10% for eyes in head, 26% for thymus in thorax, and 76% for kidneys in abdomen/pelvis. In most of the organs, the correlation between dose and water equivalent diameter was significantly improved in ATCM compared to FTC acquisitions (P < 0.001). The proposed method employs size specific CTDIvol-normalized organ dose coefficients for ATCM-activated and FTC acquisitions in pediatric CT. These coefficients are substantially different between ATCM and FTC modes of operation and enable a more accurate assessment of patient-specific organ dose in the clinical setting.