Self-assembly of peptides into fibrils and other morphologies has attracted much attention in many fields, especially in nanofabrication, pathology and biochemistry. In this paper, self-assembly of GAV-9 peptide in organic solvents, ethanol and acetone, was investigated using atomic force microscopy (AFM) and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The results indicated that GAV-9 self-assembled into various nanostructures in both solvents after deposited and evaporated on mica. Fibrils with beta-sheet conformation were observed in both solvents when the peptide concentration was higher than 280 microM. However, ordered fibrils with beta-sheet conformation were formed in ethanol, but not in acetone, with a peptide concentration ranging from 7 microM to 28 microM. We attribute the formation of various nanostructures to the different physicochemical properties of the polar organic solvents on the self-assembly of GAV-9 peptide.