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Staphylococcal isolates from specimen submitted to the Medical Microbiology laboratory of Ahmadu Bello University Teaching Hospital, Zaria were collected over a period of 6 months (February-July 2012), characterized by microbiological standard procedures and the S. aureus small colony variant (SCV) isolates were isolated. The antibiotic susceptibility pattern of the isolates was determined by the Kirby-Bauer-CLSI modified disc agar diffusion (DAD) technique. The SCV isolates were assessed for the carriage of four virulence genes; sdrE (putative adhesin) icaA (intracellular adhesin) hlg (hemolysin), Cna (collagen adhesin). A total of 258 non-duplicate staphylococcal isolates made up of 219 (84%) S. aureus and 39 (15%) coagulase-negative staphylococci (coNS) where obtained. A total of 48 (22%) isolates were determined to be S. aureus SCV mainly from wound/abscess (31%). S. aureus SCV isolates were generally resistant to all the nine antibiotics tested with only minimal sensitivity to tigecyclin (10.4%) and ciprofloxacin (18.8%). Statistically, there was no significant difference between the microbial load and the different antibiotics that were used, (P ≥0.05). None of the S. aureus SCV isolates carried the four virulence genes which were tested in this study. The results have therefore proved that S. aureus small colony variant exist in our environment and they are more resistant to most antimicrobial agent than their wild type.