This baseline study evaluated prevalence and antibiotic resistance of food-borne bacteria as conventional poultry facilities transition to organic practices. Poultry litter, feed, soil, water samples and poultry questionnaire responses were collected from 10 conventional and 10 organic-transitioning poultry houses from March to June 2008. Enterococcus spp. (n=260) and Salmonella spp. (n=100) isolates were identified to species level and antimicrobial susceptibility testing was performed using the Sensititre® system. Statistical analyses were performed using STATA 10. Prevalence of Enterococcus spp. on organic-transitioning and conventional poultry farms was 100%; and prevalence of Salmonella spp. was 100% and 40%, respectively. Enterococcus isolates from conventional poultry houses displayed significantly higher percentages of resistance for 9 antibiotic agents compared to organic-transitioning isolates. Conversely, Salmonella spp. isolated from both conventional and organic-transitioning poultry houses exhibited similar antibiotic resistance patterns. Baseline findings suggest importance of poultry production practice in prevalence and antibiotic resistance patterns of food-borne bacteria.