The recently introduced bilinear indices are applied to the QSAR/QSPR studies of heteroatomic molecules. These novel atom-based molecular fingerprints are used to predict the boiling point of 28 alkyl-alcohols and partition coefficient, specific rate constant and antibacterial activity of 34 2-furylethylenes derivatives. The obtained models are statistically significant and show rather very good stability in a cross-validation experiment. The comparison with other approaches exposes a good behavior of our method in this QSPR studies. The obtained results suggest that with the present method, it is possible to obtain a good estimation of physical, chemical and physicochemical properties for organic compounds.