Two techniques for the integration of temperature sensors in microchannels have been developed and compared. The two designs rely on different measuring principles, the first deriving from integrated circuit silicon microfabrication and the second being based on conventional commercial sensors. The proposed experimental approach offers a broad flexibility of applications, overcoming the material limitations typical of microelectronic integrated sensors. Heat transfer of gases in microchannels was studied to validate and characterize the integrated sensor systems, and the results were also compared with computational fluid dynamics (CFD) simulations. Whereas conventional sensors result as a simpler and robust technology, integrated circuit-based sensors offer higher sensitivities and potentials.