Purpose: We examine the ultrastructural changes reported to be present in dysfunctional bladders and determine whether they can be used as a predictor of urodynamic diagnosis in a clinical setting. Materials and Methods: Subjects who required urodynamic diagnosis and cystoscopy as part of clinical management were recruited for this study. After urodynamic diagnosis cases were classified into 1 of 5 dysfunction groups as normal bladder outflow obstruction, idiopathic sensory urgency, obstruction with detrusor instability and pure detrusor instability. A detrusor muscle biopsy was taken from the lateral wall of the bladder at cystoscopy for subsequent electron microscopy. Results: Of the 27 cases 6 were normal, 9 had bladder outflow obstruction and detrusor instability, 8 had pure detrusor instability and 4 had idiopathic sensory urgency. The obstructed group showed the myohypertrophy pattern previously reported. In contrast to previous reports, abnormal junctions were found in all patients. For each patient the ratios of abnormal-to-normal junctions were calculated. Mean and standard error ratios were 1.1 ± 0.1, 2.7 ± 0.2, 6.1 ± 1.2, 13.3 ± 4.4 for normal, idiopathic sensory urgency, obstruction with detrusor instability and pure detrusor instability, respectively (p = 0.0003, 0.0042 and 0.04). Conclusions: There are distinct morphological changes in the detrusor associated with bladder dysfunction. The ratio of abnormal-to-normal junctions is a novel measurement and can be used to predict urodynamic dysfunction. Ultrastructural studies may be useful as an adjunct in the diagnosis of bladder dysfunction.