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Species have been lost at unprecedented rates. Because only a small fraction of the threatened taxa have been managed under human care, contrasting the characteristics of taxa that have, and have not been targeted to ex situ conservation can reveal the reach of this conservation strategy, and can indicate its main challenges. Here we investigated whether the level of threat, diet, body mass, phylogeny, and previous presence in captivity due to non-conservation purposes could be potential parameters accounting for the occurrence of Brazilian threatened avian species and subspecies in ex situ conservation facilities and for their eligibility to organized ex situ conservation plans. Using Bayesian phylogenetic comparative models we found positive effects of body mass and phylogeny, and a negative effect of insectivorous diet in the occurrence of the taxa in non-conservation facilities. The previous presence in non-conservation facilities, together with phylogeny, diet, and body mass were the main parameters accounting for the occurrence of the threatened taxa in ex situ conservation facilities, and the previous presence in non-conservation facilities and phylogeny explained the existence of organized ex situ conservation plans. This is evidence that conservation breeding facilities have mostly harbored threatened confiscated birds than choosing them based on scientific criteria. We suggest that investing in the development of husbandry techniques, especially for insectivorous passerines, and choosing taxa based on scientific criteria are important challenges that should be on the agenda of conservation managers.