The wealth of protein sequence and structure data is greater than ever, thanks to the ongoing Genomics and Structural Genomics projects. The information available through such efforts needs to be analysed by new methods that combine both databases. One important result of genomic sequence analysis is the inference of functional homology among proteins. Until recently sequence similarity comparison was the only method for homologue inference. The new fold recognition approach reviewed in this paper enhances sequence comparison methods by including structural information in the process of protein comparison. This additional information often allows for the detection of similarities that cannot be found by methods that only use sequence information.