Acetohydroxyacid synthase (AHAS, E.C. 126.96.36.199) is the first enzyme in the branched-chain amino acid biosynthesis pathway. Five of the most widely used commercial herbicides (i.e. sulfonylureas, imidazolinones, triazolopyrimidines, pyrimidinyl-benzoates, and sulfonylamino-cabonyl-triazolinones) target this enzyme. The catalytic subunit of Arabidopsis thaliana (At) AHAS has previously been co-crystalized with sulfonylureas and imidazolinones. The structures showed these two classes of herbicides bind to the enzyme by significantly different mechanisms of induced fit. This raises questions as to how the other three classes of commercial herbicides associate with the enzyme, and what changes occur in the uninhibited enzyme in order to bind the herbicides. Here, we have determined the crystal structures of At AHAS in the absence of inhibitor (2.9 Å resolution), and in complex with two pyrimidinyl-benzoates and two sulfonylamino-carbonyl-triazolinones (2.7–2.8 Å resolution). These new structures show that the herbicide-binding site in uninhibited At AHAS is already highly ordered and folded. This is in contrast with unliganded Saccharomyces cerevisiae AHAS, which shows that the critical regions for herbicide binding are disorded. In addition, these herbicides cause a side reaction that leads to the breakdown of the cofactor ThDP. The structures provide an unprecedented understanding of the mechanism of inhibition of plant AHAS by the commercial herbicides and new insights into the molecular basis of weed resistance that results from application of these herbicides. These data then can be exploited to design more sophisticated AHAS inhibitors as advanced herbicides.