The synthesis of 4,5-diamino derivatives of pyrimidine and pyrimido[4,5-d]pyrimidines is presented. The antibacterial and antifungal activity of the compounds was investigated on nine selected bacterial species, comparing the changes in the chemical structure with increase in the bioactive properties. The investigations have shown that the obtained derivatives of pyrimido[4,5-d]pyrimidines and especially the compounds reveal interesting antibacterial 6e and antifungal 6d activity.