Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages. Our analysis includes the cavity diameter, number of windows, window diameters, and average molecular diameter. Molecular dynamics trajectories of molecular pores can also be analyzed to explore the influence of flexibility. We present the methodology, validation, and application of pywindow for the analysis of molecular pores, metal–organic polyhedra, and some instances of framework materials. pywindow is freely available from github.com/JelfsMaterialsGroup/pywindow.