The paper presents the synthesis of 1,2,3,7-tetraaryl-1,2,3,4-tetrahydropyrimido[4,5-d]pyrimidines. The structures of the obtained compounds were confirmed by crystallographic and spectroscopic analyses, and their antibacterial activity was tested on 9 selected strains, comparing chemical structure changes with increased microbiological activity. It was confirmed that aromatic residues in the hydrogenated pyrimidine ring constitute a significant element influencing antibacterial activity. Electronegative radicals increase microbiological activity, but decrease solubility of the compounds. Therefore, substituents should be selected in a manner ensuring a balanced effect. The presented crystal structure of 6f includes two stereoisomers, which we decided to isolate and compare the microbiological properties in further studies.