Females in most bird species engage in extra-pair copulations. Although this behaviour is widespread, benefits for females of doing so are less understood. The most widely accepted hypothesis is that they improve their previous choice of social partner and gain genetic benefits for their offspring. Some evidence for this comes from studies that find that extra-pair young (EPY) have greater fitness than their half-sibs. However, this might be also caused by maternal, non-genetic effect, a possibility that remains largely untested. Here we test whether EPY are laid in larger eggs or eggs laid early in the laying sequence in the collared flycatcher (Ficedula albicollis). The size of eggs bearing EPY and within-pair young (WPY) did not differ, however, EPY were laid in early eggs and consequently hatched earlier than WPY. As hatching asynchrony is a strong determinant of offspring size and survival in many species, including collared flycatcher, our results suggest that a caution is needed when paternal genetic effects are to be inferred from comparison of naturally occurring half-sibs.