Multi-drug resistance of pathogenic bacteria often results from the over-expression of the multi-drug efflux system. AcrB is a major multi-drug efflux transporter protein in E.coli that exports wide variety of drugs, antibiotics and toxic compounds. We have solved the crystal structure of AcrB at 3.5 angstrom resolution. Three AcrB monomers are organized as a trimer. Each monomer is composed of 12 transmembrane α-helices and a 70 angstrom protruding hydrophilic region in periplasmic space. This is the first crystal structure of drug transporter, and also the first atomic-level structure of a secondary transporter which driven by proton motive force across the plasma membrane.