Cordierite can incorporate various molecules in small structural micropores occurring in channels parallel to the c-axis. The types of molecules and their concentrations can reveal information about the environment in which the cordierite was formed. The molecular species of 27 natural cordierites, covering a wide range of chemical composition and sampled from different petrologic environments, were analyzed using powder FT-IR spectroscopy. The orientations and behavior of both H2O and CO2 in the micropores in cordierites were studied using both published data and from the measurements in this work. Using the IR spectra, a calibration curve for a determination of the concentration for both molecular H2O and CO2 was made. The interaction between molecular H2O and CO2 with the cordierite structure was studied. The results indicate no or little interaction between these molecular species and the framework. In order to characterize further the molecular species and their degassing behavior in cordierite, the molecular species were studied using high vacuum-high temperature extraction experiments with simultaneous thermal gravimetry and mass spectrometry. H2O and CO2 are the predominant molecular species, but He, Ar, N2, H2S, SO2 and aliphatic hydrocarbons were also detected. The temperature-dependent degassing profiles for H2O and CO2 and the kinetics of H2O and CO2 loss in cordierite was also studied and are reported