Genomics is on the verge of creating a large number of proteins for structure determination. Since X-ray crystallography is the main tool for determining protein structure, a corresponding large number of X-ray diffraction experiments will have to be performed. However, X-ray analysis is labor intensive so that the question of which protein crystal to choose for X-ray analysis from the vast pool of candidates becomes important from an economics standpoint. It is desirable to have a rapid and efficient method to score protein crystals regarding their likelihood for being of diffraction quality. We propose intrinsic protein fluorescence as a scoring tool and report preliminary data that demonstrate correlation between fluorescence spectra of single crystals and their internal order as determined by X-ray crystallography. Specifically, fine structure and maxima of fluorescence emission spectra of lysozyme, hyaluronate lyase, and germination protease crystals were found to correlate with resolution and mosaicity determined by X-ray analysis. If the correlation exhibited by these three proteins reflects a general relationship for the majority of protein crystals, a rapid fluorescence assay for scoring crystals can be developed and adapted for a variety of configurations of high throughput crystal growth apparatus.