In the present study the antimicrobial potential of various extracts from 12 medicinal plants has been investigated in vitro on multiple antibiotic resistant pathogens and some selected protozoa isolated from poultry. The initial examination was performed on E. coli (n = 10) using disc and agar well diffusion assays. Only two plants, Peganum harmala (seeds) and Eucalyptus globulus (leaves) showed positive responses. The active extracts were also investigated against an additional 19 bacteria and the clonal cultures of three protozoa (Histomonas meleagridis, Tetratrichomonas gallinarum and Blastocystis sp.). Only Peganum harmala was found to inhibit the growth of all bacteria and protozoa at 0.38-1.55 mg/mL and 0.63-1.65 mg/mL, respectively. To investigate the potential role of alkaloids in crude extracts of Peganum harmala, four known beta-carbolin alkaloids were quantified and their antimicrobial activity was compared using a microdilution assay. Harmaline was found to be in the highest concentration followed by harmine and harmalol, whereas harmane could not be detected. The activity of the pure alkaloids was in the order harmane > harmaline > harmalol > or = harmine for all bacteria, while for protozoa, it was different depending on the microorganism. It is concluded that Peganum harmala or its alkaloids could probably be used for the control of antibiotic resistant isolates of bacteria as well as protozoa.