The stability toward decarboxylation of six protein amino acids with functionally substituted side chains [phenylalanine (Phe), serine (Ser), threonine (Thr), proline (Pro), histidine (His), and methionine (Met)] were studied with an FT-IR spectroscopy flow reactor at pH(25) 1.5-8.5, T = 270-340 degreesC, and P = 275 bar. The first-order (or pseudo-first-order) rate constants and Arrhenius parameters were obtained on the basis of the rate of CO2 formation. The decarboxylation rates of Phe, Ser, Thr, Pro, and Met are independent of pH in the range of 3-8.5. At pH 1.5-3, a maximum rate constant occurs at about 2.5. His has a different pH-rate profile. At its natural pH(25) (7.44), the decarboxylation rate reaches a minimum, but increasing or decreasing the pH increases the rate. The activation energies and preexponential factors for the decarboxylation of the protein amino acids cover a wide range. However, a strong correlation between E-a and In(A) (the kinetic compensation effect) exists, which implies that the amino acids share the same mechanism or at least the same rate-determining step regardless of the side chain. Combining the observations about decarboxylation, deamination, and dehydration, we discuss the effects of the side chains on the hydrothermal stability of protein amino acids in terms of their structures.