Oligo(phenylene-ethynylene), self-assembled monolayers on Au(1 1 1) have been studied with scanning tunneling microscopy. The oligo(phenylene-ethynylene) molecules are adsorbed in a flat-lying orientation. Time-resolved scanning tunneling microscopy measurements reveal that the molecules continuously switch back and forth between two nearly degenerate configurations. The energy difference between the two configurations is 22 ± 5 meV and the activation barrier for the transition from the low-energy configuration to the high-energy configuration is 0.65 ± 0.03 eV. A statistical analysis of the residence times revealed that the switching process is stochastic. We propose that the two level switching is due to a torsional mode of the central phenyl ring.