Many identification and relatedness studies methods had been commonly used for epidemiological studies in microbiological laboratories. Apart from phenotypic methods, genotypic are also often used. The aim of this study was to compare, obtained by PFGE chromosomal DNA patterns of methicillin-resistant S. epidermidis strains isolated from clinical material. 46 methicillin-resistant S. epidermidis strains were included in this study. Most of them were isolated from wound swabs (65.2%) and catheters (19.6%) from different surgical clinics (76.1%). To identify strains and receive biochemical profiles, ID 32 Staph tests and GPI cards of Vitek 1 system were used. Pulsed-field gel electrophoresis and Tenover et al. interpretation were used to compare chromosomal DNA patterns of examined strains. 44 and 42 PFGE patterns of chromosomal DNA were received, using visual interpretation classifying two pairs of strains as the same, two pairs as closely related and three pairs as probably related. Strains classified as identical and similar in visual evaluation were indistinguishable in Molecular Analyst DST interpretation, probably due to tolerance in bands location pattern. Strains probably related in visual interpretation represent at least 96% similarity in Molecular Analyst DST but different susceptibility and biochemical profiles obtained by ID 32 Staph and Vitek 1. PFGE analysis had foremost capacity to distinguish methicillin-resistant S. epidermidis strains using visual interpretation and Molecular Analyst DST (Bio-Rad) program and seems to be useful method in epidemiological studies. Strains with the same PFGE pattern, had different susceptibility and biochemical profiles.