Objective@#To compare and quantify the differences in size-specific dose estimates (SSDE) obtained by effective diameter and water-equivalent diameter from the central slice of the scan range in head CT examination.@*Methods@#A total of 111 consecutive adultpatientswho underwent head CT examination were enrolled in this study. All of CTDIvol values in the dosereport were documented. The dataset was assigned into group A and group B, based on the individual size-dependent conversion factors (f) of effective diameter (deff) and water-equivalent diameter (dw) at the central slice multiplied by normalized volume computed tomographydose index (CTDIvol ) respectively. Body size, f and SSDE were calculated. With SSDEgross served as the reference level, the performance of SSDEdeff and SSDEdw was evaluated.@*Results@#Statistically significant differences were found in body size (t=47.587, P<0.05) and f(z=-9.242, P<0.05) between group A and group B. Statistically significant difference also existed in SSDE (t=-46.687, P<0.05), (56.20±2.66) and (53.49±2.48) mGy for group A and group B respectively. Strongly positive correlation was shown in body size (r=0.873, R2 =0.761) and SSDE (r=0.974, R2 =0.949) between group A and group B(all P<0.05). Positive correlation was also found between SSDEdeff and SSDEgross(r=0.900, R2 =0.809), SSDEdw and SSDEgross (r=0.904, R2 =0.817, all P<0.05). Mean absolute difference was 2.34 and 0.78 mGy, for SSDEdeff vs. SSDEgross and SSDEdw vs. SSDEgross respectively; mean absolute relative difference was 4.38%, 1.40%; root mean square difference was 1.17 mGy (2.17%), 1.06 mGy (1.91%). Interquartile range and full range of SSDEdeff and SSDEdw were 3.22 vs. 2.39 mGy, 13.65 vs. 12.48mGy, respectively. A less degree of variation was observed in SSDEdw than that in SSDEdeff.@*Conclusions@#SSDEdw values based on the water-equivalent diameter at the central slice of the scan range got better agreement with those derived from all slices, which could serve as a simpler and more valid indicator to represent the average value of size-specific dose estimates of the whole scan range in head CT examination.