Molecular orientation is critical to the properties of fibers, yet analysis of electrospun nanofibers of small diameters is challenging due to limited spatial resolution of the characterization techniques. In this paper, we report a quantitative analysis by the polarized atomic force microscopy-infrared technique of molecular orientation in individual electrospun nanofibers. A correction factor was first introduced to account for the energy difference between the IR radiations in the parallel and perpendicular polarizations, and then polyvinylidene fluoride and polyacrylonitrile nanofibers with diameters of several hundred nanometers were investigated. By measuring the IR dichroic ratios for the fibers of different thicknesses, we showed that the molecular orientation in the individual fibers produced under identical conditions increased with decreasing fiber diameter.