The antimicrobial activities of sheep milk yoghurt prepared by different starter strains were evaluated against different pathogenic microbial strains using different techniques. Sheep yoghurt prepared with LAB starters YC-183 and probiotic starter ABT-3, manifested anti-Staphylococcus aureus activities. Most antimicrobial activities were associated with yoghurt soluble proteins fraction and originating from high molecular weight peptide fragments (more than 3000 Dalton) if the milk yoghurt was pretreated at 85ºC / 10 min, but from low molecular weight peptides (lower than 3000 Dalton) if the milk used was pretreated at 96ºC/ 5 min. Yoghurt prepared by all starter cultures exhibited antimicrobial activity against E.coli HB101. This activity was more pronounced in the casein fraction of the yoghurt prepared after heating at 96ºC/5 min especially those prepared with ABT-3 culture. Comparable or slightly lower activities were associated with soluble protein fractions separated from different starter-yoghurt prepared from sheep milk preheated at 85ºC/10 min which loosed their activities after ultrafiltration through 3000 Da membrane. This inhibitory action was particularly evident against Staphylococcus aureus and E. coli HB101. An antibacterial peptide against E. coli which generated from β-casein by the proteolytic system of starter culture of yoghurt was isolated and this peptide has a molecular weight 4.6KDa.