Xanthogranulomatous epididymitis is an uncommon but benign process, characterized by tissue destruction and the accumulation of abundant foamy macrophages mixed with lymphocytes and plasma cells. The pathogens generally found to cause xanthogranulomatous inflammation have been Proteus and E. coli. We identified such a pathogen by sequencing divergent regions of 16S rRNA, followed by pathogen-specific-PCR using alr, ipaH, ial, and iuc primer pairs in DNA microdissected from an H&E stained slide. We report here three cases of xanthogranulomatous epididymitis caused by E. coli.