The purpose of this study is to accurately and effectively automate the calculation of the water‐equivalent diameter (normalDnormalW) from 3D CT images for estimating the size‐specific dose. normalDnormalW is the metric that characterizes the patient size and attenuation. In this study, normalDnormalW was calculated for standard CTDI phantoms and patient images. Two types of phantom were used, one representing the head with a diameter of 16 cm and the other representing the body with a diameter of 32 cm. Images of 63 patients were also taken, 32 who had undergone a CT head examination and 31 who had undergone a CT thorax examination. There are three main parts to our algorithm for automated normalDnormalW calculation. The first part is to read 3D images and convert the CT data into Hounsfield units (HU). The second part is to find the contour of the phantoms or patients automatically. And the third part is to automate the calculation of normalDnormalW based on the automated contouring for every slice (normalDW,all). The results of this study show that the automated calculation of normalDnormalW and the manual calculation are in good agreement for phantoms and patients. The differences between the automated calculation of normalDnormalW and the manual calculation are less than 0.5%. The results of this study also show that the estimating of normalDW,all using normalDW,n=1 (central slice along longitudinal axis) produces percentage differences of −0.92%±3.37% and 6.75%±1.92%, and estimating normalDW,all using normalDW,n=9 produces percentage differences of 0.23%±0.16% and 0.87%±0.36%, for thorax and head examinations, respectively. From this study, the percentage differences between normalized size‐specific dose estimate for every slice (nSSDEall) and nSSDEnormaln=1 are 0.74%±2.82% and −4.35%±1.18% for thorax and head examinations, respectively; between nSSDEall and nSSDEnormaln=9 are 0.00%±0.46% and −0.60%±0.24% for thorax and head examinations, respectively.PACS number(s): 87.57.Q‐, 87.57.uq‐