We compared quantitative susceptibility mapping (QSM) with wave-CAIPI 9 × (QSM_WC9 ×) with reference standard QSM with GRAPPA 2 × (QSM_G2 ×) in two MR scanners. We also compared detectability of microbleeds in both QSMs to demonstrate clinical feasibility of both QSMs. This prospective study was approved by the institutional review board and written informed consent was obtained from each subject. Healthy subjects were recruited to evaluate intra-scanner reproducibility, inter-scanner consistency, and inter-sequence consistency of QSM_G2 × and QSM_WC9 × at 2 MR scanners. Susceptibility values measured with volume of interests (VOIs) were evaluated. Patients who were requested for susceptibility weighted imaging were also recruited in this study to measure microbleeds on QSM_G2 × and QSM_WC9 × . The number of microbleeds was compared between two QSMs. Total 55 healthy subjects (male 34, female 21, 38.3years [23-79]) were included in this study. We investigated reproducibility and consistency of QSM_WC9 × by comparing reference standard QSM_G2 × in two MR scanners in this study, and high correlation (ρ, 0.93-0.97) and high intraclass correlation coefficient (ICC) (0.97-0.99) were obtained. Sixty patients (male 30, female 30; age, 55.4years [21-85]) were finally enrolled in this prospective study. The ICC of the detected number of microbleeds between QSM_G2 × and QSM_WC9 × was 0.99 (0.98-0.99). QSM_WC9 × and reference standard QSM_G2 × in two MR scanners showed good reproducibility and consistency in estimating magnetic susceptibilities. QSM_WC9 × and QSM_G2 × were also comparable in terms of microbleeds detection with good agreement of raters and high ICC.