Numerical and experimental techniques were used to study the physics of flow separation for steady internal flow in a 45° junction geometry, such as that observed between two pipes or between the downstream end of a bypass graft and an artery. The three-dimensional Navier–Stokes equations were solved using a validated finite element code, and complementary experiments were performed using the photochromic dye tracer technique. Inlet Reynolds numbers in the range 250 to 1650 were considered. An adaptive mesh refinement approach was adopted to ensure grid-independent solutions. Good agreement was observed between the numerical results and the experimentally measured velocity fields; however, the wall shear stress agreement was less satisfactory. Just distal to the ‘toe’ of the junction, axial flow separation was observed for all Reynolds numbers greater than 250. Further downstream (approximately 1.3 diameters from the toe), the axial flow again separated for Re [ges ] 450. The location and structure of axial flow separation in this geometry is controlled by secondary flows, which at sufficiently high Re create free stagnation points on the model symmetry plane. In fact, separation in this flow is best explained by a secondary flow boundary layer collision model, analogous to that proposed for flow in the entry region of a curved tube. Novel features of this flow include axial flow separation at modest Re (as compared to flow in a curved tube, where separation occurs only at much higher Re), and the existence and interaction of two distinct three-dimensional separation zones.