AbstractSeveral sequences, including conventional gradient‐echo sequence (e.g., FLASH), gradient‐echo echo‐planar imaging (EPI), T2* prepared ultrafast gradient echo technique (TurboFLASH), and T2*‐weighted spiral sequence, are currently used for T2*‐weighted functional magnetic resonance imaging. This paper presents a comparison of FLASH, gradient‐echo EPI, and T2*‐prepared TurboFLASH. Experimental results have demonstrated that these sequences have different susceptibility to physiologic fluctuation, which is likely the dominant source of noise. EPI images exhibit the lowest relative fluctuation, while images obtained by FLASH and TurboFLASH, respectively, display similar relative fluctuation. Functional maps generated using these sequences are comparable but exhibit different sensitivity to activation from large vessels. Consequently, interpretation of activation results from various maps should take into account the difference in