This review article briefly introduces the applications of bacterial cyclohexanone monooxygenases to the enantioselective oxidations of organic sulfur compounds to sulfoxides. High enantioselectivities are observed in the sulfoxidation of alkyl aryl sulfides, disulfides, dialkyl sulfides, cyclic and acyclic 1,3-dithioacetals. The oxidation of alkyl aryl sulfides with flavin dependent microorganisms extends the synthetic interest of this class of enzymes.