To get this certification we recently just had all of our birds tested for Salmonella pullorum. The disease affects hatchlings early on and is something you don't want on the farm. To read more about the testing or getting your flock tested the link below gives more specific information about how to get it done. Happy hatching!
http://www.aphis.usda.gov/animal_health/animal_dis_spec/poultry/
From the USDA site: Raising chickens, ducks, turkeys, and other types of poultry--whether done for profit or pleasure--entails undertaking the serious responsibility of disease prevention. Probably the greatest single factor which limited the early expansion of the U.S. poultry industry was the disease known as Bacillary White Diarrhea (BWD), caused by Salmonella pullorum. This disease, later called pullorum disease, was rampant in poultry and could cause upwards of 80 percent mortality in baby poultry. Poultrymen recognized the problem, but were unable to manage it until the causative organism was discovered by Dr. Leo Rettger in 1899 and a diagnostic blood test was developed by Dr. F.S. Jones in 1913.