The adsorption mechanism of alpha-sexithiophene (alpha-6T) on the clean Si(100)-(2x1) surface has been investigated using scanning tunneling microscopy (STM) and first principles electronic structure calculations. We find that at submonolayer coverage, the alpha-6T molecules are not stable and dissociate into monomers. We observe two different configurations of the monomers and have discussed the corresponding adsorption geometries based on theoretical calculations. The calculations elucidate how the fragments are absorbed on the surface, giving rise to the observed STM images. With increasing coverage, the STM images show the existence of complete alpha-6T molecules. In addition, results of the adsorption behavior of alpha-6T molecules on the H-passivated Si(100)-(2x1) surface are reported. On this surface the molecules are highly mobile at room temperature due to the weak molecule-substrate interaction. The STM results also indicate that they can easily be anchored at the defect sites.