OBJECTIVE: To assess the spatial organization of two proteins involved in the Sertoli cell junctional complex in men with primary seminiferous tubule failure. DESIGN: Retrospective study. SETTING: Medical research institute. PATIENT(S): Sixteen men total, six with meiotic arrest, seven with the Sertoli cell-only phenotype, and three with normal spermatogenesis. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Differences in claudin-11 and connexin-43 organization as detected using confocal microscopy. RESULT(S): In men with primary seminiferous tubule failure, four organizational patterns (I-IV) were recognized and quantified for claudin-11. Across these patterns, claudin-11 changed from a basal filamentous staining pattern to a punctate staining pattern with diffuse localization throughout the entire epithelium. Similar changes in staining patterns for connexin-43 were observed. Major differences were seen in the spatial organization of claudin-11 and connexin-43 in tubules from control men compared with tubules with primary seminiferous tubule failure, but we observed no differences in the spatial organization of these proteins in tubules from men with meiotic arrest and Sertoli cell-only phenotypes. CONCLUSION(S): The spatial organization of claudin-11 and connexin-43 is altered in men with primary seminiferous tubule failure. Disorganization of the proteins composing the Sertoli cell junctional complex may be involved in the spermatogenic impairment, possibly via loss of blood-testis barrier function.