This paper describes synthesis, spectroscopic characterization and in silico analysis of novel 5-amidinobenzimidazole derivatives designed with the aim to evaluate their antitrypanosomal activity. For the synthesis of target compounds classical methods of organic synthesis, and microwave-assisted synthesis were used. Amidinobenzimidazole hybrids (37-60) were prepared by condensation of the bisulfite adducts of the corresponding benzaldehyde derivatives (4-18, 26-34) with 4-amidino-1,2-phenylenediamine 36. Synthesis of compounds 39, 45, 46, 48, 58 i 59 was carried out under classic conditions and applying microwave irradiation. Benzaldehyde intermediates containing aryl (4-9), morpholino (10-15) and diethylamino (16-18) substituents were synthesized in microwave-assisted O-alkylation reactions from the corresponding 4-hydroxybenzaldehydes (1-3). Regioselective Cu(I)-catalysed 1,3-dipolar cycloaddition from the 4-(prop-2-ynyloxy)benzaldehydes (19-21) was used to obtain the 4-((1,2,3-triazol-4-yl)methoxy)benzaldehyde derivatives (26-34). Synthesis of unsubstituted 1,2,3-triazole derivatives (26-28) was executed by classic and microwave-assisted syntheses. 4-(1,4,5,6-Tetrahydropyrimidin-2-yl)benzene-1,2-diamine hydrochloride 36 was synthesised from the diaminobenzonitrile 35 by the Pinner method. The structures of all newly synthesized compounds were confirmed by means of 1H NMR and 13C NMR. The course of Pinner reaction preparation of amidine 36 was monitored by IR spectroscopy. ADME and pharmacokinetic properties as well as druglike nature of novel compounds were predicted by in silico approach.