Eight novel uracil-based cationic surfactants containing Schiff base species were synthesized and characterized using elemental analysis, FTIR, 1 H-NMR and 13 C-NMR spectroscopy. The surface activities of the synthesized Schiff bases and their cationic derivatives were determined based on interfacial tension measurements and partition coefficient values in water/octanol system. The synthesized Schiff bases and their cationic derivatives were evaluated as novel biocides against different bacteria and fungi strains. The results showed that the biocidal activity of the synthesized Schiff bases was considerably increased by quaternization. The influence of the cationic surfactants as biocides was increased by increasing the hydrophobic chain length and the presence of the methoxy groups. The biocidal activity was also increased by increasing the partition coefficient in water/octanol system. The structure and surface activity/ biocidal activity of the different compounds were discussed.