Purpose This study investigated the ultrastructural changes in extraocular muscles under which radioactive plaques had been placed for the treatment of uveal melanoma. Methods At the time of plaque removal, biopsies were taken from four horizontal recti that had been left in situ over plaques and from one lateral rectus muscle that had been disinserted before brachytherapy. Normal lateral recti from enucleated eyes were used as controls. Iodine-125 seeds were used with a mean total activity of 54.04 mCi, remaining for an average of 149.62 hours over the sclera. Results Muscles that had been left in situ over the radioactive plaques demonstrated a focal decrease in muscular tissue and increased fibroblasts and collagen. Electron microscopy showed increased collagen, loss of sarcoplasmic reticulum and swollen mitochondria. The disinserted muscle in the plaque group appeared unaffected. Conclusions Despite the theoretical shielding properties of plaques, leaving an extraocular muscle over the plaque may lead to several non-specific ultrastructural changes.