Vibration welding is a common process used in automotive industry to join plastic components. It allows short cycle times, does not require any surface preparation or specific additives. In addition, failure characteristics are almost unaffected when pristine polymers are welded. However, welding glass fiber reinforced polymers leads to drastic loss of such properties. Indeed, strength at break values are typically divided by two for welded composites when compared to the unwelded material. This loss of mechanical properties is generally attributed to fibers reorientation toward the squeeze flow direction in the melt layer during welding. The aim of this study is to understand in better details how the presence of fibers impacts the welding zone microstructure and how this in turns affects the mechanisms of deformation and failure of the materials . Our study focusses on three different thermoplastic polymers with different rheological behavior: PA6, PA66 and PP. Glass fiber reinforced polymers were injected at various glass fiber concentrations and welded along different edges in order to induce different initial orientations of fibers regarding to the weld plane (namely parallel and perpendicular). Welding pressure was also varied as it impacts the squeeze flow intensity during welding operation and so the reorientation of fibers. Tensile tests performed on welded samples indicate that the initial orientation of fibers has a strong effect on the failure mechanisms leading to the strength at break of the materials. In parallel, welds microstructures were studied using synchrotron microtomography. Along with fibers reorientation, fibers agglomeration and presence of voids were observed in the heat affected zone. In deep image analysis is now being performed to correlate quantitatively microstructure defects populations with mechanical properties of welded assemblies. This will lead to the identification of a reliable finite element models for the studied materials in the welded zone.