Structure and stability of the complexes formed between pyrimidine and water molecules have been completely investigated in the present study using by second order Moller-Plesset (MP2) and density functional theory (DFT) on the basis set 6-311++G(d,p). Nine reasonable geometries on the potential energy hyper surface of the pyrimidine and water are considered: two each are with two, three and four water molecules and one each with one, five and six water molecules. Optimized geometries and hydrogen binding energies for various structures have been estimated. Hydrogen binding energies and bond distances as well as the vibrational characteristics show that as the number of water molecules increases stability of the complexes increases and the bond length between N and H decreases. The ring-breathing mode ν1 of the reference system Pd was chosen as a marker band to probe the degree of hydrogen bonding.