The present invention is directed towards methods for the classification of plant embryos by the application of one or more classification algorithms to analyze digitized images and absorption, transmittance, or reflectance spectra. The methods are generally applicable and emphasize the importance of acquiring and using as much image and absorption, transmittance, or reflectance spectral information as possible, based on objective criteria. The present invention allows automated selection of embryos most suitable for further culture and rejection of those seen as less suitable.