Filial cannibalism occurs in many animal species ranging from insects to mammals, and is especially well described in teleost fishes. Numerous causes may lead to this behaviour, e.g. certainty of paternity. However, the cues males use to assess their paternity often remain unknown. One possible way to differentiate between own and foreign offspring is by using egg cues. Nevertheless, in egg-laying species, evidence for this is still scarce. In this study, male three-spined sticklebacks (Gasterosteus aculeatus), a fish with paternal care in which sneaking as well as filial cannibalism is common, were allowed to care for manipulated nests that contained different percentages of own fertilized eggs. After 7 days, embryo survival was determined. Furthermore, brood-caring as well as aggressive behaviour was measured daily. Clutches containing a higher proportion of foreign eggs were more likely to be completely cannibalized than clutches containing a lower proportion of foreign eggs, particularly when the clutch was laid early in the breeding season. However, the behavioural observations revealed no influence of paternity. The results show that paternity triggers filial cannibalism in sticklebacks and that males are able to evaluate their paternity using egg cues alone.