We present a study of the effect of misalignments in the assembly of two halves of a Ka-band serpentine waveguide (SWG) traveling-wave tube (TWT). We use the electromagnetic simulation software from Ansys, High Frequency Structure Simulator (HFSS), to characterize the structure. We focus on the frequency dependent scattering parameters, in particular the reflection coefficient, as well as the spatial distribution of the structure’s field. Our goal is to establish the sensitivity to various types of misalignments of the two halves of the structure, which ideally are joined at a plane of symmetry containing the beam tunnel axis. We have previously observed in [1] that misalignments corresponding to shifts of the two halves of the structure do not disrupt the periodicity of the structure and consequently, have little impact on the scattering parameters. The effect of these shifts on field distributions will be presented. Misalignments corresponding to rotations of the two halves disrupt the periodicity and can be expected to have a larger impact on the scattering parameters. More specifically, the type of misalignment we consider consists of rotating the top half of the SWG about an axis in the center of the SWG structure normal to the plane of symmetry. Simulations will be compared to measurements of a sample structure.