There is an increasing need for compact biodefense devices that work autonomously and consume minimal reagents. These requirements can be well met by microfluidic technologies. This review first describes the needs for biodefense, which include protection of civilian populations with detect-to-warn and detect-to-treat modalities, and the needs of the military. The different microfluidic technologies applied to each step of threat detection are then discussed. The technology areas covered are microscale 324 Jovanovich and Horn sample preparation, immunomagnetic separations, immunoassays, toxin detection, proteomics, microarrays, and microelectrophoresis. For each technology area, the potential microfluidic solutions are introduced and current relevant examples are described. For each area, the potential applications to biodefense are detailed. The present state of fully integrated microfluidic devices is reviewed. Finally, perspectives for the future are discussed.