Abstract Overview: The typing of micro-organisms in pharmaceutical factories often relies on expensive and time-consuming molecular techniques. So, the implementation of cheap, fast and reliable typing methods in the routine would speed up the investigation procedures improving the contamination control strategy. The Fourier-transform infrared (FT-IR) spectroscopy is a method that generates spectra, that enables to micro-organisms typing within 3 h. This study aimed to evaluate the FT-IR for typing S. epidermidis strains isolated from an immunobiological pharmaceutical industry in Brazil. Fifty strains were evaluated by FT-IR using IR Biotyper®. A dendrogram was created with the raw data to cluster the separation spectrum and the cut-off value was automatically calculated. Forty-four FT-IR profiles were obtained, a ratio of 1.14 strain/profile. From the five clusters formed, Cluster 1, 2 and 3 (6 strains) were isolated from environmental monitoring of air and operators (EMO). Cluster 4 (3 strains) were isolated from EMO and bioburden assays, suggesting that the environment could be the main source of bacterial contamination in the product analyzed in bioburden assay. Cluster 5 (2 strains) were isolated from EMO and a cell culture lineage used in quality control assays, suggesting that the environment could also be the main source of cell contamination. Learning Objectives: FT-IR using IR Biotyper® seems to be a promising technique for S. epidermidis strains typing and tracking possible sources of contamination in the immunobiological facility evaluated in this study. This equipment allows the creation of a specific database for each bacterial species, which can be updated continuously and used for analysis by time space of specific product groups and/or areas in the facility, among others. The methodology applied in this study can be used as part of the contamination control strategy to develop preventive and corrective measures to eliminate microbial contamination.