The search for alternative therapies for the treatment of Chagas disease presents great importance, since there are only two currently available drugs, nifurtimox and benznidazole. Both have considerable adverse effects and, in Brazil, is used only benznidazole. Nitro-heterocyclic compounds with activity against Trypanosoma cruzi, the causative agent of Chagas disease, has shown promising results. Thus, this work includes the design, synthesis, identification, evaluation of anti-T. cruzi activity of 5-nitro-2furfuriliden (IC 50 T. cruzi) and cytotoxicity of these compounds against J774 macrophages cell line (IC 50 J774). The nifuroxazide, as a lead compound, inspired the molecular modification leading to two series of furfuriliden compounds, a azometinic structure, series I, and other with oxadiazolinic structure, series II. The choice of substituents was based on the Craig's diagram, and ten substituents were selected for each series. We evaluated the activity of twenty compounds designed against T. cruzi, and the most active compounds were: 4-butyl-[N'-(5-nitrofuran-2-yl) methylene] benzidrazide (4g-IC 50 T. cruzi = 1.05 μM, SD = 0.07) and 3-acetyl-5-(4-butylphenyl)-2-(5-nitrofuran-2-yl)-2,3-dihydro, 1,3,4-oxadiazole (5g-IC 50 T. cruzi = 8.27 μM, SD = 0.42). Compared to the reference drugs, benznidazole (IC 50 T. cruzi = 22.69 μM, SD = 1.96) and nifurtimox (IC 50 T. cruzi = 3.78 μM, SD = 0.10), the compound 4g demonstrated anti-T. cruzi activity superior to both drugs. All compounds showed better activity than nifuroxazide (IC 50 T. cruzi = 120.46 μM, SD = 4.06). For cytotoxicity assays, was found for the most active compound against T. cruzi, 4g, IC 50 J774 = 28.05 μM, SD = 1.05, and for compound 5g was obtained IC 50 J774 = >400 μM, that represents the maximum concentration of the compound evaluated which did not affect the cells. Both showed good selectivity in the calculation of the ratio between the IC 50 T. cruzi and IC 50 J774. Additionally, we performed calculations of the physicochemical properties of three-dimensional structures of the compounds, followed by exploratory data analysis including hierarchical cluster analysis (HCA) and principal component analysis (PCA), which contributed to the identification of properties that influence the activity anti-T. cruzi in the series of compounds studied. The findings indicated a significant influence of ClogP and dipole moment properties, pointing out the need of a lipophilic/hydrophilic balance in the designing of novel anti-T.