The emerging interest in RNA research is due to the discovery that bacterial non-protein-coding RNAs (npcRNAs; often referred to as "non-coding RNAs") are central regulatory molecules. While single npcRNAs have been described in Staphylococcus aureus, mostly based on computational-based approaches, experimental data on npcRNAs and their impact on the formation of different phenotypes of S. aureus are missing. Consequently, two specialized cDNA libraries were constructed from total RNA collected from different growth phases of an isogenic clinical strain pair of S. aureus displaying both the normal and the small-colony variant phenotype. Overall, 142 candidates for novel npcRNAs were identified and their expression analyzed by Northern blot assays. Of these, the presence of 18 novel npcRNAs in S. aureus was experimentally confirmed. In fact, growth phase-specific regulation was detected for almost all of the novel npcRNAs, with different npcRNA expression patterns detectable for both phenotypes. Of particular interest, S. aureus phenotype-specific expression of four novel npcRNAs was documented. Thus, the presence of differentially expressed npcRNAs in S. aureus may help to understand the phenotypic variation and its associated pathogenicity.