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To compare quantitative fractional ventilation measurements from multiple breath washout imaging (MBW-I) using hyperpolarized 3He with both spoiled gradient echo (SPGR) and balanced steady-state free precession (bSSFP) three-dimensional (3D) pulse sequences and to evaluate the feasibility of MBW-I with hyperpolarized 129Xe.Seven healthy subjects were scanned using 3He MBW-I with 3D SPGR and bSSFP sequences. Five also underwent MBW-I with 129Xe. A dual-tuned coil was used to acquire MBW-I data from both nuclei in the same subject position, enabling direct comparison of regional information.High-quality MBW images were obtained with bSSFP sequences using a reduced dose (100 mL) of inhaled hyperpolarized 3He. 3D MBW-I with 129Xe was also successfully demonstrated with a bSSFP sequence. Regional quantitative ventilation measures derived from 3He and 129Xe MBW-I correlated well in all subjects (P < 0.001) with mean Pearson's correlation coefficients of r = 0.61 and r = 0.52 for 3He SPGR-bSSFP and 129Xe-3He (bSSFP) comparisons. The average intersubject mean difference (and standard deviation) in fractional ventilation in SPGR-bSSFP and 129Xe-3He comparisons was 15% (28%) and 9% (38%), respectively.Improved sensitivity in MBW-I can be achieved with polarization-efficient bSSFP sequences. Same scan-session 3D MBW-I with 3He and 129Xe has been demonstrated using a dual-tuned coil.