Glycyl-l-proline (Gly-l-Pro) is the main degradation product of collagen and is a good diagnostic tool in various pathological conditions. The aim of this work was to prepare dipeptide Gly-l-Pro labeled with 99mTc. Complex preparation was carried out under alkaline reaction conditions and its stability was assessed 10 and 120 min after preparation. The formation of two types of complex compounds was observed. High-performance liquid chromatography, paper electrophoresis, paper chromatography and thin layer chromatography were employed to monitor the formation of different complexes. Molecular modeling (semi-empirical method) was used to design their structure and composition. First complex cI with formula [TcO(Gly-l-Pro)]−1 is unstable. After 120 min cI is completely transformed to complex cII with formula Tc(Gly-l-Pro)3.