This article summarizes our previously achieved and published results. The method for the determination of bacterial volatile fatty acid patterns (VFA) in clinical samples was elaborated. It employs gas chromatography (GC), solvent extraction or head-space solid phase microextraction (SPME). This method was validated by analyses of reference bacterial strains. After cultivation in defined media, aerobic and facultative anaerobic bacteria provided profiles with a low or none acid content, while anaerobic bacteria provided characteristic but medium-dependent profiles with a higher acid content. This method was used for the analyses of clinical samples of total 375 blood cultures, 205 suppurative and apyogenous exudates, and 210 bronchoalveolar lavages (BALs). These analyses enabled within 30 minutes the detection of microbes, probably non-sporulating anaerobes not found by false-negative cultivation, in 11.2% of blood cultures, in 20.0% of exudates, and in 9.0 to 20.0% of BALs. Using the mass spectrometry (MS) methods, a number of other components with unclear diagnostic importance were found in BAL samples, in particular hydrogen cyanide, methanol, ethanol, hexanol, acetone, cyclohexanone, acetonitrile, formaldehyde, acetaldehyde, ethyl acetate, and other esters. Cyclohexanone, occurring mainly in BALs of patients with pneumonia, undergoing intensive care, may originate as a residual solvent from the plastic parts of the ventilation apparatus.