Background Conventional 99mTc-macroaggregated albumin (99mTc-MAA) planar scintigraphy overestimates lung shunt fraction (LSF) as compared to SPECT/CT in 90Y radioembolization treatment planning. However, the respiratory motion artifact due to the temporal mismatch between static SPECT and helical CT (HCT) may compromise the SPECT quantitation accuracy by incorrect attenuation correction (AC) and volume-of-interest segmentation. The goal of this study is to systematically assess different AC and segmentation protocols for LSF, tumor-to-normal liver (TNR), organ absorbed dose and injected activity (IA) estimation in 99mTc-MAA SPECT/CT.Methods The 4D XCAT phantom was used to simulate 10 patient anatomies with 99mTc-MAA distribution based on the clinical data, each with LSF of 5%, 10%, 15% and 20%, axial respiratory motion of 2 cm, different TNR and tumor size. An analytical projector for low energy high resolution parallel-hole collimator was used to simulate realistic noisy planar acquisitions, and 128 projections over 360o for SPECT, both modeling attenuation, scatter and geometric collimator-detector-response. Five attenuation maps, i.e., (i) HCT at end-inspiration (HCT-IN), (ii) HCT at mid-respiration (HCT-MID), (iii) HCT at end-expiration (HCT-EX), (iv) cine averaged CT (CACT) and (v) interpolated average CT (IACT) were applied for SPECT AC and segmentation in LSF, dosimetric and IA evaluation. Mid-respiratory phases were also extracted from CACT/IACT for VOI segmentation while CACT/IACT were used for AC, i.e., hybrid CT protocols.Results For LSF estimation, SPECT/CACT has the least absolute errors. Planar significantly overestimates LSF and lung absorbed dose compared to SPECT especially for LSF of 5%. SPECT-based is better than CT-based segmentation in TNR estimation. There is no statistically significant difference for different CT protocols for TNR, normal liver and tumor absorbed dose estimation. Hybrid CTs and HCT-MID performed the best for IA especially for higher LSF.Conclusions 99mTc-MAA SPECT/CT with an appropriate choice of CT protocol for AC and segmentation is superior to planar in LSF and lung absorbed dose estimation. The 4D CT protocols are recommended for AC and segmentation to alleviate respiratory artifacts and improve quantitation accuracy in 90Y radioembolization treatment planning. HCT-EX would also be a recommended choice if 4D CT is not available.