Pyrimidine and thienopyrimidine derivatives play a very important role in organic chemistry because of their wide applications as bioactive compounds with multiple biological activities. However, a literature survey revealed that the merger of different groups in the thieno[2,3-d]pyrimidine heterocyclic ring enhances its antibacterial, antifungal and anti-inflammatory activities. This encouraged us to prepare a new series of thieno[2,3-d]pyrimidine heterocyclic compounds and to test them as antimicrobial and anti-inflammatory agents. These compounds have shown remarkable activity toward fungi, bacteria, and inflammation. Thus, these compounds have been prepared by the chloroacylation of 5-amino-4-phenyl-2-(p-tolylamino) thieno[2,3-d] pyrimidine-6-carboxamide (4) using chloroacetyl chloride under neat condition to afford the target compound (6), which was used as precursor for the synthesis of a number of bioactive compounds. Thus reaction of the chloromethylpyrimidine derivative (6) with triphenylphosphine in dry benzene gave the corresponding ((4-oxo-9-phenyl-7-(p-tolylamino)-3,4-dihydropyrimido[4 0 ,5 0 :4,5]thieno [2,3-d]pyrimidin-2-yl)methyl) triphenylphosphonium chloride (7). Compounds 8a-8c and 9a-9c were obtained by the reaction of 7 with some selected aromatic aldehydes and ketones in methanol and sodium methoxide under Wittig reaction condition. The structures of the all new synthesized compounds were established on the basis of their analytical and spectral data (IR, 1 H NMR, 13 C NMR, and MS).