We conducted an investigative study to determine the prevalence and risk factors for Salmonella contamination of poultry farms in Jos, Plateau State, Nigeria. A standardized questionnaire was used to collate data on farm management practices, demographic characteristics, farm-handlers personal hygiene and clinical information from August, 2012 to April, 2013. Odds ratios were computed using bivariate analysis. Results revealed 10.9% prevalence of Salmonella species from the study using standard bacteriological methods. Farm previously contaminated by Salmonella (OR48.0; CI 95%2.40-958.0), presence of rodents (OR 11.25; CI 95% 1.19-106.13), movement from one pen to the other by farm-handlers (OR4.38; CI 95% 1.10-33.9), running and parking truck near the entrance to poultry farms (p < 0.05) and the use of untreated water (p < 0.05) were found to be independently associated with an increased risk of Salmonella infection in broiler and layer flocks. Furthermore, the results indicates that application of specific hygiene measures in the farm, such as washing of hands after tending the flocks, use of footbath disinfection when entering the poultry house, may significantly reduce the risk of Salmonella infection in chicken and farm-handlers. However, the use of antibiotics and vaccination against Salmonella were found to be protective.