Flavor preferences vary; what one enjoys may be disgusting to another. Previous research has indicated several brain regions associated with flavor preferences. However, by using different stimuli or different internal states to obtain differences in liking, results of these studies may be confounded. Therefore, we used one target stimulus (grapefruit juice) and fMRI to compare brain activation patterns between participants that either liked (n = 16) or disliked (n = 18) this stimulus. Our first aim was to investigate whether differential neural activation exists that accounts for the difference in subjective flavor preference for the target stimulus. Secondly, multivariate analysis was used to investigate whether differences in subjective liking for the target revealed similar activation patterns as differences in general liking for a sweet and bitter solution. A direct comparison of likers and dislikers of the target stimulus revealed only small differences in activations in orbitofrontal cortex (OFC) and dorsal anterior cingulate cortex (dACC). However, when using multivariate analysis, a broader activation pattern (including OFC, dACC, pregenual anterior cingulate, anterior insula and ventral striatum) was identified that discriminated likers from dislikers with an 88% success rate. Interestingly though, little overlap was found between this pattern and the pattern that discriminates liking for the sweet and bitter solutions and lesser voxels contributed to the former compared with the latter. These differences between patterns discerning innate versus learned preferences may suggest that different mechanisms are at work and highlight the importance of elucidating the neural processes of how subjective preferences are learned and acquired.