Wild (Cavia aperea) and domestic (C. porcellus) cavies pups emit high-pitched isolation whistles with individual characteristics when separated from their mother. A similar whistle is emitted only by the domestic species in response to caretaker arrival and food delivery anticipation stimuli. This study provide the first comparison of food-anticipation (FA) and pup isolation (IS) whistles in order to assess FA origins in the repertoire of domestic guinea pigs. We compared intra-individually sonographic structure of FA and IS whistles. Vocalizations emitted by three animals were analyzed. Results revealed that both calls have a harmonic structure characterized by short, high-pitched Notes, with broadband frequency spectrum uttered in fast repetitive sequences. Despite the similarity in basic structure, differences in acoustic parameters were observed. FA Notes were longer, repeated in slower rhythm, had larger bandwidth and longer and more modulated frequency in the ascending part than IS Notes. Moreover, sonographic analysis suggested that individual characteristics of IS parameters may also be present in FA calls. Findings suggest that FA is a product of domestication process derived from IS and may indicate an adjustment of domestic cavies to interaction with human beings.