For some embedded engine arrangements, the nature of the inlet distortion is influenced by the boundary layer characteristics at the inlet plane of the intake. This research presents the first quantitative assessment on the influence of inlet boundary layer thickness and asymmetry on the swirl distortion at the exit of an S-shaped intake. Measurements of high spatial and temporal resolution have been acquired at the outlet plane of the S-duct using time-resolved particle image velocimetry. When boundary layer profiles typical of embedded engines are introduced, the characteristic secondary flows at the outlet plane are intensified. Overall, the peak swirl intensity increases by 40% for a boundary layer which is 7 times thicker than the reference case. The unsteady modes of the S-duct remain, although the dominant fluctuations in the flow arise at a frequency 50% lower. When the inlet boundary layer profile becomes asymmetric about the intake centerline the peak swirl events at the hub are reduced by up to 40%. At the tip the peak swirl intensity increases by 29%. The results demonstrate that the effects of inlet boundary layer thickness and asymmetry must be carefully considered as part of engine compatibility tests for complex intakes. Nomenclature ai(t) = Temporal coefficient for i th mode in Proper Orthogonal Decomposition [ms -1 ] Ain = S-duct inlet plane area [m 2 ] Aout = S-duct outlet plane area [m 2 ] Din = S-duct inlet plane diameter [m]