New pyrrolo[2,3-d]Pyrimidines with heteroaryl substitution at 5th position through sulfur linker were synthesized incorporating putative pharmacophoric moieties like benzimidazole and benzothiazole as heteroaryl groups. Cytotoxic effect of all the compounds was carried out on HCT116 colon cancer cell lines. Compounds 6c and 6h with nitrobenzimidazole and pyrimidyl heterocycles attached at 5th position via sulfur were the most potent of all with IC50 values approximately 17.6 muM. Among the four compounds tested for apoptosis induction activity, 6c induced apoptosis in a dose dependent manner.