The sequence of the Arabidopsis genome has given us information about one plant's complement of aspartic proteinases. Using an in silico analysis based on the homology to known aspartic proteinase genes, we have uncovered 51 sequences that potentially encode these enzymes. This is substantial more than the number predicted for other eukaryotic systems. We have grouped the deduced amino acid sequences into 3 classes - typical plant aspartic proteinase, nucellin-like and atypical aspartic proteinase sequences-, depending on their putative domain organizations and their active site sequence motifs. Searching databases has revealed cDNAs or ESTs for nearly 90% of these genes. Sequence analysis using software that detects targeting signals indicates most of the predicted proteins have the expected localization in the secretory system although several of these are membrane bound. The analysis also predicts 8 chloroplast localized proteins and 2 mitochondria-localized aspartic proteinase-like proteins. The wide variety of structures and subcellular locations implies multiple functions for aspartic proteinases in plants.