Insect juvenile hormones are metabolized in numerous species of caterpillars by low abundance, highly specific esterases. Because of their role in regulating and possibly disrupting juvenile hormone titer and thus insect metamorphosis, they are of interest to developmental biologists as well as scientists interested in selective insect control. However, the enzymes have defied attempts to purify and characterize them. Juvenile hormone esterase activity can be inhibited by a variety of 3-substituted 1,1,1-trifluoropropanone sulfides. These apparent transition state analogs were used as ligands and eluting agents to purify juvenile hormone esterase from four insect species from 500-fold to over 1000-fold in high yield. After elution from the affinity column, the enzymes were radiolabeled with paraoxon and analyzed by electrophoresis, and the results demonstrate a high degree of purity. Transition state analogs may be useful for the affinity purification of other enzymes.