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Background: The histological and electron-microscopic (EM) characteristics of juvenile nasopharyngeal angiofibroma (JNA) have been described but no study has compared them with one another or with clinical features. The objective is to compare ultrastructural characteristics of JNA with clinical parameters. Methods: This prospective study included histology of 21 samples of which only 13 underwent transmission-EM. Four clinical parameters (age, duration, epistaxis, recurrence), three radiological-staging, 13 histological and 15 EM characteristics were considered. A descriptive analysis for association of these characteristics and also with clinical parameters was attempted. Furthermore statistical analysis of clinical and radiological categories with respect to frequencies of ultrastructural characteristics was also undertaken. Results: Dense-intranuclear-inclusions (DNI) and peripheral-nuclear-irregularities were universally encountered while other very prominent features were nuclear-blebs-and-pockets, myoid-features, thin-vessel-wall (TnVW), irregular-vascular-contour (IVC) and fibrous-stroma (FS). Statistical significance was obtained between recurrence with histology (p = 0.04) and Fisch staging with EM (p = 0.001). While muscle-in-vessel-wall, thick-vessel-wall, mast-cells, stellate-stromal-cells and cellular-stroma predominated in recurrent cases, the upfront disease showed predominance of scar-like-stroma, fusiform-stromal-cells, IVC, TnVW, FS, organised-collagen-bundles and less-cellular-stroma. A very unique Rod-like-structures were appreciated in the cytoplasm of the fibroblast for the first time. Conclusions: While histological parameters of recurrence need further validation, a larger sample may better define histopathological surrogate for predicting intracellular dynamics that may further correlate with underlying cellular stresses. Hence an 'ultrastructural staging' may better customise treatment protocol and prognosis. Furthermore 'characteristic' unique rods need to be further investigated along with validation of viral aetiology for DNI. [ABSTRACT FROM AUTHOR]