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The transformation of the synthesized allicin, using conventional method, the influence of ultrasound and microwaves, in different organic solvents (acetonitrile, acetone, methanol, and chloroform), at various temperatures (room temperature, 45∘C, and 55∘C) was investigated. Allicin degradation kinetic was monitored by HPLC. Allicin transformation under the effect of microwaves is faster than transformations performed under the influence of ultrasound or by conventional method. Increase of the temperature accelerates allicin transformation. Pharmacologically active compounds of (E)-ajoene, (Z)-ajoene, 3-vinyl-4H-1,2-dithiin, 2-vinyl-4H-1,3-dithiin, and diallyl disulfide were isolated from the mixture of transformation products of allicin under the influence of microwaves in methanol at 55∘C, which is according to kinetic parameters (highest values of the order of reaction and the lowest activation energy) the optimal method.