The sulphoxide group is present in various pharmacologically active agents. Recently, there has been an increased interest in the development of methodologies for the preparation of chiral sulphoxide. One of the approaches for the preparation of chiral sulphoxide is to exploit the enzymatic capacity of the microbial cells in bringing about stereospecific sulphoxidation of the achiral sulphide. In the current work, an attempt has been made to screen certain selected microorganisms for sulphoxidation of omeprazole intermediate. Bio-oxidation was performed in phosphate buffer of pH 7.6 with the resting cells of various fungi. The sulphide intermediate (concentration 1g/L) was incubated with the resting cells for 48 h at 30 °C, 160 rpm in a rotary shaker. The work up consisted simply of filtration to remove the spent mycelium, extraction of the filtrate with alkaline dichloromethane and further concentration by evaporation to get the oxidized product. Ten different species of fungi were tested for sulphoxidation, of which only two species, Aspergillus niger and Rhizopus stolonifer, showed conversion. The product was identified by TLC and LCMS, quantification was done by HPLC.