The processes of thermal decomposition of analytes in gas chromatographic (GC) columns are classified and two new examples of them are considered in details. First of them is monomolecular decomposition of monoalkyl esters of benzene-1, 2-dicarboxylic (phthalic) acid (monoalkyl phthalates). This process has the analogy in chemical reactions in solutions and it may be responsible for the toxicity of phthalates. The second example is decomposition of non-substituted hydrazones of both aliphatic and aromatic carbonyl compounds. The analytes of the second sub-group present the first example of bimolecular (second order) decomposition in a GC column: two molecules of hydrazones form stable azines and hydrazine. Besides that this process presents the particular interest, because it is accompanied by secondary chemical reactions not in an injector, but within GC column, when a by-product of decomposition is involved into secondary interaction with other constituents of the samples. It was confirmed, that visual images of all these decomposition processes on the chromatograms are rather identical and coincide with the manifestations of interconversion of isomers or tautomers. The most often expressed features of chromatographic profiles in such cases are the presence of peaks of an initial analyte and a product of its decomposition or isomerization, connected with more or less expressed diffused “plateau” or “train” between them. The decomposition processes during sample preparation prior to chromatographic separation or in the heated injector of GC instrument are not accompanied by such features. Despite of the rather “exotic” character of the examples considered, the knowledge of them seems to be useful for better revealing the analogous situations in chromatographic practice. Thermal instability of analytes is the principal restriction of GC separation of reactive compounds and we cannot eliminate it for objective reasons. However, in some cases we can evaluate the temperature limits of chromatographic columns, which should not be exceeded during GC separation of instable compounds. The simplest (low boiling) homologs of thermally unstable compounds are often characterized by “normal” boiling point at atmospheric pressure (T
b, °C) without decomposition, that means the possibility of their GC analysis unambiguously. Therefore, we can select such T
b values as GC and/or GC–MS temperature limit (T
lim) for other members of series of thermally unstable homologs. If GC separation is carried out not in isothermal, but in temperature programming conditions, so-called retention temperature (T
R) of unstable analytes should not exceed the evaluated T
lim value.