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In sexually size-dimorphic species, brood sex composition may exert differential effects on sex-specific mortality. We investigated the sex-specific mortality and body condition in relation to brood sex composition in nestlings of the black-billed magpie Pica pica. Neither significantly sex-biased production at hatching nor overall sex-biased mortality during the nestling period was found. Sex-specific mortality as a function of brood sex composition, however, differed between female and male nestlings. We found higher mortality for females in male-biased broods and higher mortality for males in female-biased broods, a phenomenon that we call ‘rarer-sex disadvantage’. As a result, fledging sex ratios became more biased in the direction of bias at hatching, a phenomenon that cannot be readily explained by previous hypotheses for sex-specific mortality. Two temporal variables, fledging date and laying date, were also correlated with sex-specific mortality: female nestlings in earlier broods experienced higher mortality than male nestlings whereas male nestlings in later broods experienced higher mortality. We suggest that this unusual pattern of mortality may be explained by adaptive adjustments of brood sex composition by parents, either through the effects of a slight sex difference in offspring dispersal patterns on parental fitness, or owing to sex differences as regards the benefits of early fledging.