Heat Transfer and Thermal Management have become important aspects of the developing field of uTAS systems particularly in the application of the the uTAS philosophy to thermally driven analysis techniques such as PCR. Due to the development of flowing PCR thermocyclers in the field of uTAS, the authors have previously developed a melting curve analysis technique that is compatible with these flowing PCR thermocyclers. In this approach a linear temperature gradient is induced along a sample carrying microchannel. Any flow passing through the microchannel is subject to linear heating. Fluorescent monitoring of DNA in the flow results in the generation of DNA melting curve plots. This works presents an experimental technique where DNA melting curve analysis is used to measure the thermal resistance of microchannel substrates. DNA in solution is tested at a number of different ramp rates and the di®erent apparent denaturation temperatures measured are used to infer the thermal resistance of the microchannel substrates. The apparent variation in denaturation temperature is found to be linearly proportional to flow ramp rate. Providing knowledge of the microchannel diameter and a non-varying cross-section in the direction of heat flux the thermal resistance measurement technique is independent of knowledge of substrate dimensions, contact surface quality and substrate composition/material properties. In this approach to microchannel DNA melting curve analysis the difference between the measured and actual denaturation temperatures is proportional to the substrate thermal resistance and the ramp-rate seen by the sample. Therefore quantitative knowledge of the substrate thermal resistance is required when using this technique to measure accurately DNA denaturation temperature