AbstractThin films of lamellar and cylindrical block copolymers are popular systems for low‐cost nanolithography. To be useful as nanoscale templates, the lamellae or cylinders must be oriented perpendicular to the substrate. Domain orientations are usually characterized by microscopy measurements of the film surface, but these techniques cannot detect tilted, bent, or tortuous domains in the film interior. We report a simple method to quantify out‐of‐plane disorder in thin films of block copolymers based on a variant of grazing‐incidence small angle X‐ray scattering (GI‐SAXS). A typical GI‐SAXS experiment illuminates the center of a substrate‐supported film at a grazing angle of incidence (near the film/substrate critical angle), and the strong reflected signal is interpreted with the distorted‐wave Born approximation. In a new approach, the beam footprint is moved to the far edge of the sample, allowing the acquisition of a transmission pattern. The grazing‐incidence transmission data are interpreted with the simple Born approximation, and out‐of‐plane defects are quantified through analysis of crystal truncation rods and partial Debye‐Scherrer rings. Significantly, this study demonstrates that grazing‐incidence transmission small angle X‐ray scattering can detect and quantify the buried defect structure in thin films of block copolymers. © 2013 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013