Auditory functional magnetic resonance imaging (fMRI) studies are limited by the presence of noise produced by echo planar imaging (EPI). The current study quantifies the effect of MR scanner noise on psychophysical measures of the perception of loudness and on measures of tonotopy, the representation of auditory frequencies within the auditory cortex. Seven normal hearing adults were examined using tones of 5 different auditory frequencies (250, 500, 1,000, 2,000, 4,000 Hz) of equal loudness. Using an imaging protocol with peak MR scanner noise at 1,460 Hz, the perception of loudness and detectable fMRI activity in response to a 1-kHz tone was less compared to other frequencies. When the imaging protocol was changed such that peak MR scanner noise occurred at 2,080 Hz, the perception of loudness and detectable fMRI activity in response to a 2-kHz tone was less compared to other frequencies. The reduction in the measured fMRI activity for tones near scanner frequencies may be due to an inflated scanner-induced baseline at those frequencies. In addition, fMRI activity decreased with increasing frequency, possibly due to the upward spread of masking of low-frequency, high-intensity tonal stimuli or the proximity of low-frequency core and belt areas of the auditory cortex. These results demonstrate the direct effect of scanner noise and high-intensity tonal stimuli on measurements of auditory cortex tonotopy. Hum. Brain Mapping 22:341–349, 2004. © 2004 Wiley-Liss, Inc.