OBJECTIVE: To assess the difference in absorbed organ dose and image quality for head-neck CT angiography using organ dose modulation compared with 3D smart mA modulation in different body mass indices (BMIs) using an adaptive statistical iterative reconstruction (ASiR-V) algorithm. METHODS: Three hundred patients underwent head-neck CTA were equally divided into three groups: A (18.5 kg/m(2) <= BMI < 24.9 kg/m(2)), B (24.9 kg/m(2) <= BMI < 29.9 kg/m(2)) and C (29.9 kg/m(2) <= BMI <= 34.9 kg/m(2)). The groups were randomly subdivided into two subgroups (n = 50): A1-A2, B1-B2 and C1-C2. The patients in subgroups A1, B1 and C1 underwent organ dose modulation with the ASiR-V algorithm, while other patients underwent 3D smart mA modulation. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of all head-neck CT angiography images were calculated. Images were then subjectively evaluated. Mean values of several indices including dose-length product (DLP) were computed. The DLP was converted to the effective dose (ED). SNR, CNR and ED in groups A, B, and C were compared in statistical data analysis. RESULTS: SNR, CNR, and subjective image scores show no statistical differences in three groups (P > 0.05). However, there is significant difference of ED values (P < 0.05). For example, in subgroup A1 mean ED values are 15.30% and 23.66% lower than those in subgroup A2 at thyroid gland and eye lens, respectively. Similar patterns also exist in groups B (B1 vs. B2) and C (C1 vs. C2). CONCLUSIONS: Using organ dose modulation and applying the ASiR-V algorithm can more effectively reduce the radiation dose in head-neck CT angiography than using 3D smart mA modulation, while maintaining image quality. Thus, using organ-based dose modulation has the additional benefit of reducing dose to the thyroid gland and eye lens.