Background: Acinetobacter species are non-fermentative, aerobic, gram-negative coccobacilli, widely distributed in hospitals considered as an important opportunistic pathogen responsible for a variety of nosocomial infections. Multiple drug resistant (MDR) strains of Acinetobacter have created therapeutic problems worldwide. Antibiotic resistance in Acinetobacter species is a new emerging problem in Iran. The aim of the present study was to determine the antimicrobial susceptibility of Acinetobacter species isolated from clinical specimens in educational hospital, in Kashan university of medical sciences. Materials and Methods: This descriptive study was carried out on sixty Acinetobacte species isolated from patients in Beheshti hospital. At the species level conventional biochemical tests were used for the identification of isolates. The strains were isolated from blood (58.3%), urine (13.3%), cerebrospinal fluids (8.3%), trachea (8.3%), sputum (8.3%), and pleural fluid (3.3%). For determination of susceptibility, Acinetobacter baumannii ATCC 19606 (11B) and Acinetobacter lwoffli ATCC (13A) strains were used as quality controls. Antimicrobial susceptibility testing was performed on all 60 isolates according to the standard method established by the CLSI (formerly NCCLS). In this analysis, MDR was defined as presence of resistance to three or more classes of antibiotics. PCR was used for the detection and amplification of antibiotic resistance genes. PCR products were resolved on agarose gel (2.0%), stained with ethidium bromide, and then photographed by UV. A 100 bp DNA ladder was used to assess PCR product. Results: Forty-eight isolates of Acinetobacter baumannii, six isolates of Acinetobacter lwoffli and six isolates of other Acinetobacter species were isolated from patients. Thirty-five (58.3%) men and 25 (41.7%) women with the mean age (±SD) of 39.27 (±19.20) years enrolled in the study. Acinetobacter species demonstrated the highest resistance to amikacin, tobramicin, ceftazidime, ciprofloxacin, piperacillin/tazobactam, doxycycline, SXT/TMP, minocyclin, levofloxacin, imipenem and sulbactam/ampicilln, respectively. MDR rate was 66.7%. The positive rate of the resistance genes for aphA 6, aacC1, ADC-7, OXA SET C, aadA 1 and aadB were 39 (65%), 38 (63.3%), 34 (56.7%), 32 (53.3%), 32 (53.3%), 25 (41.7%), and 2 (3.3%), respectively. Conclusion: In the present study, A cinetobacter baumannii was the most common isolate among the patients. Acinetobacter species demonstrated the highest resistance rate to amikacin, tobramicin and ceftazidime. The genetic analysis revealed the presence of aphA6, aacC1 and ADC-7 genes in all of the strains and aphA6 in resistance to amikacin, gentamicin, kanamycin, and neomycin. Another gene aacC1 suggests the resistance to gentamicin and Bla ADC including seven genes encoding B- lactamase (bla -ADC-1, bla-ADC-2, bla-ADC-3, bla-ADC-4, bla-ADC-5, bla-ADC-6, bla-ADC-7). Because of nosocomial spread and resistance to more groups of antibacterial agents, Acinetobacter species pose a threat for hospitalized patients.