| BARC | Beltsville Agricultural Research Center |
| BATFE | Bureau of Alcohol, Tobacco, Firearms and Explosives |
| BAU | Behavioral Analysis Unit |
| BBG | Broadcasting Board of Governors |
| BEA | Bureau of Economic Analysis |
| BECON | Biomedical Engineering Consortium (defunct as of 11/08) |
| BEP | Bureau of Engraving and Printing |
| BER | Biological and Environmental Research |
| BERA | Business & Economics Research Advisor |
| BES | Basic Energy Sciences |
| BEST | Biomonitoring of Environmental Status and Trends (changed to I&M) |
| BFRL | Building and Fire Research Laboratory |
| BHPr | Bureau of Health Professions |
| BIA | Bureau of Indian Affairs |
| BIE | Bureau of Indian Education |
| BIF | Bank Insurance Fund (merged into DIF) |
| BIMAS | BioInformatics Molecular Analysis Section |
| BIS | Bureau of Industry and Security |
| BJA | Bureau of Justice Assistance |
| BJS | Bureau of Justice Statistics |
| BLM | Bureau of Land Management |
| BLS | Bureau of Labor Statistics |
| BMDO | Ballistic Missile Defense Organization (changed to MDA) |
| BNL | Brookhaven National Laboratory |
| BNQP | Baldrige National Quality Program |
| BOP | Federal Bureau of Prisons |
| BOR | Bureau of Reclamation |
| BPA | Bonneville Power Administration |
| BPC | Best Practices Committee |
| BPD | Bureau of the Public Debt |
| BPHC | Bureau of Primary Health Care |
| BRAC | Defense Base Closure and Realignment Commission |
| BRB | Benefits Review Board |
| BRD | Biological Resource Division |
| BRFSS | Behavioral Risk Factor Surveillance System |
| BRS | Biotechnology Regulatory Service |
| BSE | Bovine Spongiform Encephalopathy (Mad Cow Disease) |
| BTA | Business Transformation Agency |
| BTOP | Broadband Technology Opportunities Program |
| BTS | Bureau of Transportation Statistics |
| BVA | Board of Veterans Appeals |
| BXA | Bureau of Export Administration (changed to BIS) |
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