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Annapolis Junction is an unincorporated community in Howard County, Maryland. Its population at the 2000 census was 40.
In present day Annapolis Junction, the historic and still busy CSX (former B&O) railroad line runs north to south, Maryland Route 32 runs east to west, various office warehouses lie to the west, and facilities relating to Fort Meade lie to the east. The Federal Bureau of Prisons operates its Mid-Atlantic Regional Office in Annapolis Junction.