Upon absorption in the intestine of the host animal, the main function of short-chain fatty acids (SCFAs), mainly acetate, propionate and n-butyrate, is as metabolic energy. SCFAs, n-butyrate in particular, can also be found in the mouth. An excess of oral SCFAs may cause not only periodontal diseases but also systemic abnormalities in humans. Previously, we reported a method for simultaneous detection by gas chromatography-mass spectrometry (GC-MS) of acetate, propionate and n-butyrate in serum, urine and saliva. In the present study we used a modified version of this method to detect not only acetate, propionate and n-butyrate, but also iso-butyrate, n-valerate, iso-valerate and caproate, because the latter are suggested to be associated with periodontal diseases. Detection ranges of SCFAs were as follows; 6.25-400 µmol/L (acetate), 0.781-100 µmol/L (propionate and n-butyrate), 0.391-50 µmol/L (iso-butyrate), 0.781-50 µmol/L (n-valerate and iso-valerate) and 1.56-50 µmol/L (caproate). Furthermore, we validated the modified detection method with triple freeze-thaw-cycle recovery tests and intra-and inter-day repeatability. Freezing and thawing did not influence the concentrations of SCFAs in saliva. Upon analysis of five clinical saliva samples, it was observed that, except for n-valerate, which was detected only in two samples, all SCFAs were detected in saliva samples. To conclude, we were able to use a modified method to analyze successfully by GC-MS the salivary concentrations of SCFAs. In addition, we simultaneously detected the salivary concentrations of iso-butyrate, iso-valerate, nvalerate and caproate. This improved method was proved to be reliable to measure the concentrations of SCFAs in saliva.