In this study, a conjugate gradient method based on an inverse algorithm is applied to estimate the unknown space and time dependent forced convection heat transfer rate of two in line cylinders placed in a cross stream. While knowing the temperature history at the measuring positions near the surfaces of the cylinders, the heat transfer rate on the surfaces of both cylinders can be successfully computed. No prior information is needed on the functional form of the unknown heat transfer rate. A particular feature in this study is that the considered Reynolds number is high enough to result in an unsteady flow around the cylinders. In addition to the transient temperature field, this makes the flow field itself time dependent as well, thus adding more complexity to the numerical analysis. The accuracy of the inverse analysis is examined by using the simulated temperature measurement. Results show that an excellent estimation on the heat transfer rate and temperature distributions can be obtained for the case considered in this study. (c) 2007 Elsevier Ltd. All rights reserved.