Different types of antimicrobial peptides have been identified in seeds from different plant species. The aim of this study was to isolate and characterize peptides present in chilli pepper seeds (Capsicum annuum L.) and evaluate their toxic activities against some yeast species. Initially, proteins from seed flour were extracted in phosphate buffer, pH 5.4, for 3 h at 4 degrees C and the pellet obtained at 90% saturation with ammonium sulfate was heated at 80 degrees C for 15 min. The resulting suspension was clarified by centrifugation and the supernatant was extensively dialyzed against water; the peptide-rich extract was then named F/0-90. Cation-exchange chromatography was performed to separate low molecular mass proteins. One of the resulting fractions, named F3, enriched with basic proteins of 6-16 kDa, was submitted to reverse-phase chromatography in a C2/C18 column by HPLC, resulting in four fractions denominated RP1, RP2, RP3 and RP4. When these fractions were submitted to N-terminal sequencing, the comparative analysis in databanks revealed homology for two of these peptides, isolated from fractions RP3 and RP4, with sequences of proteinase inhibitors and 2S albumins, respectively. The F3 fraction, rich in peptides, inhibited the growth of yeasts Saccharomyces cerevisiae, Candida albicans, Candida parapsilosis, Candida tropicalis, Pichia membranifaciens, Kluyveromyces marxiannus and Candida guilliermondii. The RP3 and RP4 fractions showed high inhibitory activity against the growth of the yeast S. cerevisiae. The F3 fraction was also able to inhibit glucose-stimulated acidification of the medium by yeast cells of S. cerevisiae and to cause several morphological changes in different yeasts, such as cell wall disorganization, bud formation as well as the formation of pseudohyphae.