Offspring behavior results from the combined expression of maternal and paternal genes. Genomic imprinting, however, silences some genes in a parent-of-origin specific manner, a process that, among all animals, occurs only in mammals. How genomic imprinting affects the behavior of mammalian offspring remains poorly understood. Here we studied the effects of the loss of the paternally inherited gene Magel2 on the emission of separation-induced ultrasonic vocalization (USV) by mouse pups. Using quantitative analysis of more than one hundred thousand USVs, we characterized the rate of vocalizations as well as their spectral features from postnatal days 6 to 12 (P6-P12), a critical phase during mouse development when pups fully depend on the mother for survival. Our analyses show that Magel2 deficient offspring emit separation-induced vocalizations at lower rates and with altered spectral features. Using methods for a holistic analysis of the entire vocal repertoire of pups, we found that Magel2 deficient mice at postnatal day 8 (P8) emit USVs that resemble the vocal repertoire of wildtype mice at older ages (P10-12). These results suggest that the deficiency of this paternally inherited gene impairs the expression of separation-induced vocalization in pups, a behavior that supports pup growth and development.