The kinetics and mechanism for the solution-phase adsorption of n-alkanethiols onto gold to form self-assembled monolayers (SAMs) have been monitored in situ using atomic force microscopy (AFM). Time-dependent AFM images reveal detailed structural information about the adsorbed layer during its growth. In 2-butanol, CH3(CH2)(17)SH molecules initially adsorb on gold with the molecular axis of their hydrocarbon chains oriented parallel to the surface. As the surface coverage increases to near saturation, a two-dimensional phase transition occurs and produces islands composed of molecules with their hydrocarbon axis oriented similar to 30 degrees from the surface normal. Continued exposure to the thiol solution results in a greater number of these islands and the growth of these nuclei until a SAM is formed with a commensurate (root 3x root 3)R30 degrees structure. The growth of the lying-down phase follows a first-order Langmuir adsorption isotherm, while the phase transition is best described by a second-order reaction. The kinetics of the self-assembly process also depends on the chain length of the alkanethiol and the cleanness of the gold surface. Longer-chained thiols, such as CH3(CH2)(17)O(CH2)(19)SH, formed complete SAMs more rapidly than did shorter-chained thiols, such as CH3(CH2)(17)SH. The physisorbed, lying-down phase for CH3(CH2)(17)O(CH2)(19)SH was less homogeneous and its two-dimensional phase transition was more complicated than for CH3(CH2)(17)SH and CH3(CH2)(21)SH, as the CH3(CH2)(17)O(CH2)(19)SH molecules adopt multiple conformations. Of these, the two dominant ones an an all-trans, and another where the hydrocarbon chain adopts an all-trans conformation except for a gauche bond on both sides of the ether unit. These conformers coexist on the surface during the initial adsorption and its transition to the standing-up phase, but change to the all-trans structure in the complete SAM.