Recent studies showed prominent antimicrobial activity of various plant extracts on certain pathogenic microorganisms, therefore we prepared crude aqueous extracts of black pepper, ginger and thyme and carried out an in vitro study by measuring antimicrobial activity of these extracts using the agar well diffusion method. An in vivo study was carried out on 50 adult healthy male albino rats which were divided into 5 groups, 10 rats each. Group 1: negative control group which received saline solution intragastrically daily; Group 2: Positive control group, injected with mixed bacterial suspension of S.aureus and E.coli as a model of pyelonephritis, then received saline solution intragastrically daily; Group 3: injected with the same dose of mixed bacterial suspension, then received 100 mg/kg/day black pepper extract intragastrically; Group 4: injected with mixed bacterial suspension then received 500 mg/kg/day ginger extract intragastrically. Group 5: injected with mixed bacterial suspension then received 500 mg/kg/day thyme extract intragastrically. All groups were sacrificed after either 1 or 4 weeks. Serum and blood samples were collected for lysozyme activity estimation using agarose lysoplate, measurement of nitric oxide production, and lymphocyte transformation test as well as for counting both total and differential leukocytes and erythrocytes. Kidney samples were tested histopathologically. Both in vivo and in vitro results confirm the efficacy of these extracts as natural antimicrobials and suggest the possibility of using them in treatment procedures.