The inevitable emergence of the bacterial resistance to conventional antibiotics is the driving force for the development of novel class of anti-infectives, such as Antimicrobial Peptides (AMPs). These peptides are considered as promising drug candidates to replace and/or supplement the existing antibiotics. The rapid increasing need for the potential AMPs can be met by combining the high-throughput parallel oligonucleotide synthesis with eukaryotic protein expression system to discover novel antimicrobial peptides. The main goals of this part of the study are to show that oligonucleotides coding for AMPs can be cloned in yeast by homologous recombination, expressed and secreted by yeast cells, and screened for their activities against microbial cells. We have constructed two different expression systems in Saccharomyces cerevisiae and Pichia pastoris to investigate the expression and secretion levels of 13 and 44-amino acid long two control AMPs. Our initial results with S. cerevisiae containing GAL10-CYC1 promoter and alpha-MF secretion signal showed that while the longer peptide was expressed at high levels, the production of the 13aa peptide was quite low. The expression level of the shorter peptide was enhanced in P. pastoris when the AMP coding genes were fused with SUMO (small ubiquitin-like modifier) gene tag. We also observed that both peptides maintained their antimicrobial activities in yeast culture when tested against Gram negative and Gram positive bacteria.