Introduction: rapid detection of pathogenic organisms is crucial in diagnosis and treatment of the diseases. The aim of this study was to evaluate efficiency of Fourier transform infra-red (FTIR) in detection of common bacteria in Khanevadeh hospital and Fallahi clinic, from NEZAJA military of health organization.

Methods: we use 300 colony of bacteria from different wards of these two centers. 20 colony was finally selected using some filters. These isolates were compared with literature and reference stoked bacteria using FTIR. The software IR solution used for peak correction. Finally, biochemical methods used for re-detection of bacteria.

Results: there constituted six group of references bacteria from decomposition to the main component in the spectrum field CM^-1. There were four bacteria in the reference cluster of E.Coli, four bacteria in the reference cluster of Klebsiella, three bacteria in the reference cluster of Pseudomonas, Three bacteria in the reference cluster of Enterococcus, three bacteria in the reference cluster of Staphylococcus Aureus, and three bacteria in the reference cluster of Staphylococcus Epidermidis. Biochemical detection methods confirmed FTIR in detection of bacteria.

Conclusion: this technic for detection of bacteria was successful despite variation in bacteria structure and physiology. It may be used in some critical situation such as war, which need to rapid and exact diagnosis. FTIR method has various sensitivity and specifity which may result confusing in analysis. So it’s necessary to optimize this method using some another study.