An increasing number of studies suggest that olfaction is important for communication throughout the order of primates. Callitrichids, in particular, have well-developed olfactory systems and use anogenital glands to produce scent marks. Behavioural studies have shown that male common marmosets (Callithrix jacchus) distinguish between odours from the peri-ovulatory and luteal phase of females. However, large gaps remain in understanding the chemical underpinnings of olfactory cues. To investigate whether chemical cues vary with female fertility and reproductive quality, our study combined behavioural bioassays with chemical analyses of the anogenital odours of female common marmosets using gas chromatography-mass spectrometry. We found that cycle states, age and parity have an impact on chemical profiles and further identified affected chemical substances. Our results confirm and expand on previous behavioural evidence for cues of fertility. Our results indicate that cycle-related substances likely act as chemical cues. Males could use such olfactory fertility cues to optimize their mating effort and thereby increase their paternity certainty. This certainty could enhance paternal care for their infants. The results of our study open a promising avenue to find the metabolic pathways from which chemical cues of fertility arise and to unravel their importance during primate evolution in future comparative studies.