This paper demonstrates the effect of microfluidic system design on temperature profiles of the whole system and more specifically of the microfluidics. Computational fluid dynamics models were used to estimate the effect of some parameters on the temperature of a microsystem with a relatively small heater. The system consisted of a Poly-Ether-Ether-Ketone (PEEK) chipholder with a heater, and a glass chip, surrounded by air. The material and design of the chipholder had a dominant effect on the temperature. Bringing the heater from 22 to 80 ° C resulted in a temperature gradient of over 40 ° C over the length of the chip at fluid level. Due to slow heating, quick switching of temperature is not possible. The steady state temperature profile at fluid level can be changed by adapting the geometry and material of the chipholder. By including the system’s thermal properties in microfluidic system design desired temperature profiles can be obtained. Computer models, such as described in this paper can be used to design a system which thermal behaviour matches the process requirements for the intended use.