A self-assembled monolayer of dodecanethiol grown on Au(111) substrate has been annealed to form different structural phases: a higher density (root 3 X root 3)R30 degrees phase, a lower density (8.5 x root 3) stripe phase, and a disordered mixed phase. The electrical properties of each phases have been studied by using scanning tunneling spectroscopy. The current-voltage curves measured on the disordered phase were less reproducible than those measured on the two well-ordered phases. Molecular resolution STM image obtained on the stripe phase shows that the structural instability of the alkyl chain of the stripe phase affect the current flow through the molecule. Our study shows that the ordering and structural stability of the molecules are very important in stable measurement of the electrical properties of the molecular films. (c) 2005 Elsevier B.V. All rights reserved.