Numerical investigation of flow and heat transfer in a rectangular duct with a built-in circular tube has been carried out for a Reynolds number of 1000 and blockage ratio of 0.44. Since the heat transfer in the duct is dictated by the flow structure, the present study is directed toward characterization of the flow structure. To this end, the topological theory shows the promise of becoming a powerful tool for the study of the flow structure. Computations show helical vortex tubes in the wake and existence of horseshoe vortices. The w component of velocity is surprisingly large in front and in the near wake of the tube. The limiting streamlines on the tube and the bottom-plate reveal a complex flow field. The separation lines as well as singularity (saddle and nodal) points have been investigated. The iso-Nusselt number contours and the span-averaged Nusselt number in the flow passage shed light on the heat transfer performance in the duct.