The one-step method for preparation of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-ones by interaction of 5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxylic acid with ortho-pnenylediamines using 1,1'-carbonyldiimidazole as a coupling-reagent has been developed. The procedure proposed allows to obtain easily the target products using common reagents and solvents; and it also requires the simple isolation methods. The selectivity of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-one interaction with benzyl chlorides in DMF-К 2 СО 3 conditions has been studied using the NOESY spectroscopic method and alternative synthetic approaches; it has been determined that the reaction occurs at position 3 of the thieno[2,3-d] pyrimidine system. The study of the antimicrobial activity by the agar diffusion method for the compounds obtained has shown that 6-(1H-benzimidazol-2-yl)-3-benzyl-5-methylthieno[2,3-d]pyrimidin-4(3H)-ones reveal the antimicrobial activity against the strains of Escherichia coli, Proteus vulgaris, Pseudomonas aeruginosa; while the compound with unsubstituted position 3 appeared to be inactive against these strains of microorganisms. However, this compound exhibited the higher inhibitory activity against the Candida albicans fungi.