We report three cases of bilateral microsporidial keratitis, which is an unusual presentation. All three patients presented with bilateral, simultaneous, asymmetrical, deep stromal corneal infiltrates with symptoms ranging from 5 to 12 months. Predisposing factors were noted in two of three patients. Corneal scrapings for microbiology and histopathology of corneal tissue revealed microsporidial spores from both eyes of all patients. There was no response to medical therapy and all underwent bilateral corneal transplantation. Case one additionally had recurrences in the graft and underwent repeat keratoplasties and eventually keratoprosthesis. Microsporidial stromal keratitis is a possible cause of keratitis in cases of very long-standing, indolent, culture-negative, deep stromal corneal infiltrates. So far, this infection has been reported as unilateral; however, we report these cases of bilateral infection, which is rare. Corneal transplantation is the preferred line of management due to lack of response to medical therapy.