Avian communal breeding systems generate alternative behavioural strategies for females, resulting in differences in reproductive success. Identifying eggs of different females in such systems is problematic, however, due to egg destruction before incubation, difficulty of capturing adults, and/or inaccuracy of egg identification based on egg morphometry. Here, we describe a technique that uses electrophoresis of yolk proteins to determine egg ownership, which we applied to communally breeding guira cuckoos (Guira guira). Validation of the method included identical yolk protein banding patterns in all eggs of the same female, but different patterns in eggs of different females in budgerigars (Melopsittacus undulatus), and identical patterns in yolk follicles of the same females in guira cuckoos. We applied the protocol to 195 guira cuckoo eggs from 34 joint nests in 2 years. All multiple guira cuckoo eggs laid on the same day in single nests had distinct banding patterns of yolk proteins, practically eliminating the possibility of more than one female being represented by the same pattern. Some identical banding patterns were repeated in different days within a nesting bout, indicating that some females laid several eggs in shared nests. Identical patterns occasionally occurred in renestings of groups, indicating that some females lay eggs in consecutive nestings. Yolk protein electrophoresis is a useful tool to identify egg maternity in other circumstances, such as polygynous mating systems with joint nests and intraspecific parasitism. Additionally, it is an alternative method for species where electrophoresis of egg white proteins does not show sufficient polymorphism.