The prevalence of Salmonella associated mortality at hatching was investigated in three hatcheries in Jos, central Nigeria. Their susceptibility to antimicrobial agents was also evaluated. S. Kentucky and S. Hadar were isolated. While half of the isolates were from internal organs, 26.7% came from meconial swabs of dead-in-shell embryos, 17.8% from intestinal samples and 4.4% from egg shells. S. Hadar is known to colonise only the gut and is classified as non-invasive, but in this study 82% were obtained from internal organs which suggests that infections with this serotype may also cause invasive disease. Antimicrobial susceptibility tests showed a high prevalence of antimicrobial resistance in the study area with complete resistance to gentamycin, enrofloxacin, nalidixic acid, tetracycline and streptomycin and substantial resistance to triple sulphur and ciprofloxacin. Six multiple resistance profiles were recorded with a high level of multiple resistance to quinolones. Quinolone resistance has implications for veterinary and human therapy as their misuse in poultry could lead to the emergence of resistant animal and zoonotic pathogens.