The current study highlights on the synthesis and characterization of aqua-complexes of the fac-[M(CO)3]+ (M = Re and 99mTc) core with pyrimidine-4,6-dicarboxylic acid (H2pmdc) and its monoester 6-(ethoxycarbonyl)pyrimidine-4-carboxylic acid (Hetpmdc), which are the model for future design of imaging and therapeutic radiopharmaceuticals. Complexes [M(CO)3(OH2)(Hpmdc)] (M = Re (1) and 99mTc (2)) were formed from the reaction of H2pmdc with [Re(CO)5Br] in water and aqueous solution of [99mTc(CO)3(OH2)3]+ respectively. The reaction of [Re(CO)5Br] with H2pmdc in ethanol (EtOH) has also studied and led to the complex [Re(CO)3(OH2)(etpmdc)] (3), where etpmdc−is 6-(ethoxycarbonyl)pyrimidine-4-carboxylate anion which was formed from the mono-esterification of H2pmdc in parallel with its coordination to the fac-[Re(CO)3]+ unit. The complex [99mTc(CO)3(OH2)(etpmdc)] (4) was formed in parallel with 2 by reacting H2pmdc with aqueous solution of [99mTc(CO)3(OH2)3]+ and ethanol. The chemical identification of 1 and 3 was achieved by using 1H NMR, 13C NMR, IR, ESI-MS and elemental analysis. Complex 3 was furtherly identified by using single crystal X-ray crystallography. The structural similarities of 1 and 2 was assessed by coinjection of both complexes in the HPLC with UV/Vis detection coupled with a γ-detector followed by comparison of retention times of the γ-peak of 2 and the UV-peak of 1 which allowed unambiguous identification of 2. Similarly, the formation of complex [99mTc(CO)3(OH2)(etpmdc)] (4) in parallel with 2 was assessed by coinjection of complexes 1 and 3 with the product from the reaction of H2pmdc with aqueous solution of [99mTc(CO)3(OH2)3]+ and ethanol in the same HPLC as one used for the structural identification of 2 followed by comparison of retention times of the γ-peaks of 2 and 4 and the UV-peaks of 1 and 3.