Substituted phenols, including chlorophenols, are important analytes, particularly in the context of environmental analysis. Chlorophenols are formed during the disinfection of drinking water by chlorination and are important water pollutants. Gas chromatography–mass spectrometry (GC-MS) is an important method for the analysis of chlorophenols. Retention indices are used in GC-MS analysis to improve the accuracy of identification. Our research reveals that the retention indices currently available for substituted phenols are erroneous in a number of cases. We report reliable retention index values for pentafluorophenol, 5-methoxy-2-nitrophenol, 4-cyanophenol (stationary phase: 5%-phenyl-polymethylsiloxane), 3-methoxyphenol, 2-chlorophenol, 3-chlorophenol, 4-chlorophenol, 2,3-dichlorophenol, 2,5-dichlorophenol, 2,6-dichlorophenol, 3,4-dichlorophenol, 3,5-dichlorophenol, 2,3,5-trichlorophenol, 2,3,6-trichlorophenol, 2,4,5-trichlorophenol, and 2,4,6-trichlorophenol (stationary phase: polyethylene glycol modified with 2-nitroterephthalic acid). The structures of the standard samples were confirmed, and measurements were performed under various conditions. The analysis of the causes of the incorrect records appearing in the well-known NIST database was also carried out.