Studying pup isolation calls of wild rodents provides background for developing new early-life animal models for biomedical research and drug testing. This study discovered a highly complex acoustic phenotype of pup isolation calls in 4–5-days-old Mongolian hamsters Allocricetulus curtatus. We analysed the acoustic structure of 5010 isolation calls emitted in the broad range of frequencies (sonic, below 20 kHz, and ultrasonic, from 20 to 128 kHz) by 23 pups during 2-min isolation test trials, one trial per pup. In addition, we measured five body size parameters and the body weight of each pup. The calls could contain up to three independent fundamental frequencies in their spectra, the low (f0), the medium (g0) and the high (h0), or purely consisted of chaos in which the fundamental frequency could not be tracked. By presence/absence of the three fundamental frequencies or their combinations and chaos, we classified calls into six distinctive categories (Low-Frequency-f0, Low-Frequency-chaos, High-Frequency-g0, High-Frequency-h0, High-Frequency-g0+h0, High-Frequency-chaos) and estimated the relative abundance of calls in each category. Between categories, we compared acoustic parameters and estimated their relationship with pup body size index. We discuss the results of this study with data on the acoustics of pup isolation calls reported for other species of rodents. We conclude that such high complexity of Mongolian hamster pup isolation calls is unusual for rodents. Decreased acoustic complexity serves as good indicator of autism spectrum disorders in knockout mouse models, which makes knockout hamster models prospective new wild animal model of neurodevelopmental disorders.