We investigated the implicit preference in terms of food portion in obesity using the affective priming paradigm. Primes representing different portions of fast food (small, medium and large) were used to assess participants’ readiness to respond to a positive or negative target word. A self-reported affective rating scale of food portion and a portion judgment task were administered to determine the explicit preference for food portion and portion misperception, respectively. The results of the affective priming paradigm showed an implicit preference for large food portions in the obese group. No implicit preference in terms of food portion was found in the non-obese group. The explicit preference measure of food portion demonstrated a rather negative attitude for large portions in the obese group, whereas the non-obese group reported no explicit preference in terms of food portion. Thus, unlike the non-obese group, the obese group showed clear discrepancies between implicit and explicit preferences in terms of food portion: obese participants demonstrated an implicit, but not an explicit preference for large food portions. These results could not be attributed to a misperception of food portion, as revealed by the portion judgment task. The current findings suggest that social desirability might conceal self-reported preference in terms of food portion and/or that obese individuals are less aware of their internal preferences.