Nanostructured dielectric waveguides are of high interest for biosensing applications, light emitting devices as well as solar cells. Multiperiodic and aperiodic nanostructures allow for custom-designed spectral properties as well as near-field characteristics with localized modes. Here, a comparison of experimental results and simulation results obtained with three different simulation methods is presented. We fabricated and characterized multiperiodic nanostructured dielectric waveguides with two and three compound periods as well as deterministic aperiodic nanostructured waveguides based on Rudin–Shapiro, Fibonacci, and Thue–Morse binary sequences. The near-field and far-field properties are computed employing the finite-element method (FEM), the finite-difference time-domain (FDTD) method as well as a rigorous coupled wave algorithm (RCWA). The results show that all three methods are suitable for the simulation of the above mentioned structures. Only small computational differences are obtained in the near fields and transmission characteristics. For the compound multiperiodic structures the simulations correctly predict the general shape of the experimental transmission spectra with number and magnitude of transmission dips. For the aperiodic nanostructures the agreement between simulations and measurements decreases, which we attribute to imperfect fabrication at smaller feature sizes.