The purpose of this study was to compare 3 T and 1.5 T fMRI results during emotional music listening. Stimuli comprised of psychoacoustically balanced instrumental musical pieces, with three different affective expressions (fear, neutral, joy). Participants (N=32) were split into two groups, one subjected to fMRI scanning using 3 T and another group scanned using 1.5 T. Whole brain t-tests (corrected for multiple comparisons) compared joy and fear in each of the two groups. The 3 T group showed significant activity differences between joy and fear localized in bilateral superficial amygdala, bilateral hippocampus and bilateral auditory cortex. The 1.5 T group showed significant activity differences between joy and fear localized in bilateral auditory cortex and cuneus. This is the first study to compare results obtained under different field strengths with regard to affective processes elicited by means of auditory/musical stimulation. The findings raise concern over false negatives in the superficial amygdala and hippocampus in affective studies conducted under 1.5 T and caution that imaging improvements due to increasing magnetic field strength can be influenced by region-specific characteristics.