For sexual selection to operate in monogamous species, males of poor quality in some factor like age, ornamentation, condition or aggressiveness, should lose paternity compared with higher quality males. We tested this idea in an Iberian population of pied flycatchers (Ficedula hypoleuca). Microsatellite analysis of 67 broods revealed moderate levels of extra-pair paternity (22.4% of broods, 7.5% of young). In a sample of 58 broods for which the caring male was identified, a higher paternity loss was associated with younger males, males that were less aggressive during territorial intrusion tests performed before the commencement of laying, and with males that showed higher levels of corticosterone metabolites in faecal samples collected at the end of the nestling period. Plumage darkness, forehead patch size and condition were not related to paternity loss. Paternity loss is more related to behavioural or physiological traits than to morphological ones in this population.