We compared two methods that have been used to assess cuckoldry in birds, i.e. DNA fingerprinting and comparison of heritability of morphological traits between the putative parents. DNA fingerprinting confirmed that the putative father had sired all young in 53 broods of great reed warblers Acrocephalus arundinaceus, from which 72 young became recruits in our study area in subsequent years. On the same data set, we found the heritability of both tarsus length and wing length between males and their offspring to be lower than between females and their offspring. In several studies, a lower heritability value between males and their putative offspring as compared to females and offspring has been interpreted as a result of cuckoldry. In the present study, heritability was estimated between offspring (measured as adults) and their genetic parents, as confirmed by DNA fingerprinting. This suggests that maternal effects may explain why tarsus length and wing length in the offspring are more similar to their mother than to their father. The present study then violates one of the basic assumptions of the heritability method, i.e. a similar contribution from the mother and the father to the expression of offspring traits. Whenever phenotypic traits (e.g. tarsus length and wing length) are under maternal influence, the method of comparing the heritability of such traits between the parents would over-estimate the frequency of cuckoldry. Because this kind of maternal effects are very difficult to control for, our study questions the heritability method as a reliable tool for revealing levels of extra-pair paternity.