Reproductive disorders are responsible for significant economic losses in canary aviculture due to embryo and newborn chick mortality. Most of the time, deaths are caused by bacterial pathogens, however little published data exist about the prevalence of bacterial isolates that are identified during diagnostic protocols. This study reports on data collected from previous investigations carried out on cloacal swabs (n 456), unhatched eggs (n 52), and dead newborn chicks (n 68) collected from canary aviaries with a history of reproductive disorders. Of the examined samples, 41% were positive for the presence of pathogenic or potentially pathogenic bacteria, with particular regard to Gram negative species during bacteriological investigations. The most prevalent microorganisms were Gram-negative (55%). A predominance of Klebsiella, Escherichia, and Pantoea genera was observed. These are usually associated to pathological conditions in pet birds. Among Gram-positive bacteria, Bacillus spp. and Staphylococcus spp. were most prevalent. The antimicrobial susceptibility testing carried out on bacterial isolates showed a multiple resistance, especially against amoxycillin, erythromycin, spiramycin, tiamulin, and tylosin. This study represents a first attempt to provide an update on microbial causes of embryonic and neonatal mortality in canary aviaries in Italy; in addition, it provides further understandings about the efficacy of antimicrobial therapy.