Three binuclear Cu(II) complexes of two pyrimidine derived Schiff base ligands, 2-S-methyl-6-methyl-4-formyl pyrimidine-N(4)-ethyl thiosemicarbazone (HL1) and salicyl hydrazone of 2-hydrazino-4,6-dimethylpyrimidine (HL2), have been prepared. HL1 produces a bis(μ-thiolato) Cu(II) complex co-crystallizing with its mononuclear analog, [Cu2(L1)2(NO3)2][ Cu(L1)(NO3)] (1). On the other hand HL2 shows versatility by producing two different classes of binuclear Cu(II) complexes, a bis(μ-phenoxo) complex [Cu2(L2)2(NO3)2] (2) and another a (μ-4,4′-bipyridyl) complex, [Cu2(L2)2(μ-4,4′-bipyridyl)(NO 3)2] (3) under suitable conditions. All the three complexes show distorted square pyramidal geometry around each Cu atom but to a varied extent. Magnetic behavior of complex 1 shows that it is strongly ferromagnetic in nature whereas compounds 2 and 3 are weakly antiferromagnetic in nature. A magnetostructural correlation study combined with molecular modelling on complexes 1 and 2 has thrown light on the difference on magnetic interaction between the Cu atoms in these two complexes. Various factors that may be responsible for such differences are also explored. A novel and potentially useful pH dependant conversion of 3 to 2 has also been noticed. © 2008 Elsevier Ltd. All rights reserved.