Introduction: S. aureus produces more than 32 extracelleular molecules which include a number of virulence factors, toxins, enzymes and haemolysins, which allow it to adhere to surface, invade or avoid the immune system and in addition causes toxicity to the host. Virulence factors like coagulase, thermonuclease and Panton Valentine Leukocidin (PVL) are all secreted. We investigated the distribution and expression of PVL and thermonuclease in clinical isolates of S. aureus. Spontaneous sequence variations were observed in the fem genes of clinical isolates of S. aureus (data under communication) and we investigated if this would impact the secretion of thermonuclease and PVL. Materials and Methods: Genomic DNA was isolated from157 S. aureus clinical isolates and screened for fem, nuc and pvl through PCR. To evaluate whether the sequence variations in fem genes had any effect on the expression of pvl, we randomly selected 43 fem (fem A, B and X) variants from the 109 pvl positive isolates and measured pvl transcript by qPCR. The isolates were genotyped for nuc by PCR and the transcript was measured by qPCR while DNAase secretion was screened by methyl green DNA agar plate method. Results: 109 (77%) out of 157 isolates were pvl PCR positive. PVL expression was marginally down regulated when compared with the reference gene in these variants. Almost all isolates were nuc-PCR positive. No remarkable change in the expression of thermo nuclease was observed among the fem sequence variants. Conclusion: Variations in the nucelotide sequences of fem A, B and X genes were observed in several clinical isolates of S. aureus. These variations did not affect the secretion of coagulase, thermonuclease and transcription of pvl. PVL has long been known as virulence factor associated with and a molecular marker for CA-MRSA. However, our study has shown a relatively high prevalence of pvl in S. aureus isolated from hospital acquired infections.