Purpose.To describe corneal intrastromal epithelial cysts and present a minimally invasive surgical technique successfully used to treat such a lesion.Methods.A 5-year-old girl with a progressive, vision-threatening, intrastromal corneal opacity in the left eye is described. The patient had a history of accommodative esotropia and bilateral medial rectus recession two years before presentation. A presumptive diagnosis of an epithelial cyst secondary to iatrogenic seeding of the limbal corneal stroma was made. Because of documented growth toward the visual axis and a decrease in best-corrected visual acuity, surgical treatment was initiated. The cyst was incised and debrided through a 2.0-mm, partial-thickness, limbus-parallel, clear corneal incision.Results.Cytologic analysis of the cyst contents showed intact and degenerated epithelial cells, thereby confirming the diagnosis. The cyst walls were scraped through the nonenlarged incision, and irrigation resulted in nearly complete clearing of the opacity. Stable vision and no recurrences were documented with 21 months of follow-up.Conclusion.This minimally invasive surgical approach may be a good alternative to previously described treatments for intrastromal corneal cysts.