A TOTAL of 350 samples were collected from different sites located in three governmental hospitals in Cairo, Handwashing sink was the most contaminated site followed by Computer keyboards and ultrasonic machines. According to viteck, bacterial isolates were identified as Staphylococcus aureus, S. saprophyticus, Bacillus cereus, B.subtilis, Klebsiella pneumonia, Acnietobacter baumanii, Pseudomonas auerignosa and Escherichia coli. Fungal isolates such as Aspergillus niger, Aspergillus fumigatus, Rhizopus stolonifer, Fusarium oxysporum, Cladosporium herbarum, Penicillium melanoconidium, and etc., were identified by macro and micro morphological characteristics. S. aureus and K.pneumonia were the most common isolated bacteria with percentage (44.2&24.7%) respectively, while A.niger was the most common isolated fungus with percentage (13%). Synthetic antimicrobial agents are widely used to fight microbial infections with some limitations and toxicity, consequently, many researches focused on new antimicrobial substances from natural plants. Antimicrobial activity of both natural (Eucalyptus leaves and Garlic extracts) and synthetic antimicrobials (Chloramphenicol, Amoxicillin, fluconazole and Amphotericin B) were tested against isolated microbial species using agar disk diffusion method. B. cereus was the most sensitive bacterial species to garlic extract with 45mm inhibition zone diameter while S.aureus and B.cereus were the most sensitive species to Eucalyptus extract with 35&30mm , respecively. On the contrary both of natural extracts possess very weak activity against isolated fungal pathogen.