From a clinical viewpoint, staphylococcal small-colony-variants (SCVs) may be characterized as Janus-faced pathogens: While the intracellularly persisting SCV phenotype is associated with chronic/relapsing infections, SCVs may cause less tissue damage because of their low exotoxin production compared to the normal Staphylococcus aureus phenotype. Thus, objective methods to define the phenotype status in vivo would be of substantial interest in the future. In general, the detection of clinical SCVs is hampered by the fact that they are difficult to recover and to identify. Whereas the classical approach to identify SCVs is necessarily based on the cultivation on solid media to determine the pin-point colony size, the reduced/absent hemolysis/pigmentation and to analyze the auxotrophism, alternative phenotypic methods, such as the Fourier-transform infrared (FTIR) spectroscopy, may offer solutions to identify a given phenotype independent from the environment of the staphylococcal cells. This is of particular interest because clinical SCVs frequently exhibit an unstable phenotype, i.e., reversion into the normal phenotype may occur. A reversion in broth media rapidly leads to overgrowth of the SCV population and is not directly traceable. Whereas the normal phenotype fulfils the criteria for standardized susceptibility tests, SCVs falls into the category of “troublesome” microorganisms. Susceptibility testing of SCVs is challenging because they grow slowly even under optimal culture conditions and their resistance properties differ from those of their clonally identical parent strains. A quantitative PCR-based approach to analyze the susceptibility of SCVs towards antibiotic compounds may serve as verifiable objective surrogate marker instead of conventional susceptibility testing.