PURPOSE: To examine the evidence that a series of cases of diffuse lamellar keratitis (DLK) after laser in situ keratomileusis (LASIK) was caused by a type of marker pen. SETTING: Eye Institute, Auckland, New Zealand. METHODS: During a 10-week period, 522 consecutive LASIK procedures were performed using a 60 Hz IntraLase femtosecond laser (IntraLase Corp.) to create the LASIK flap and a 217Z 100 Hz excimer laser (Bausch & Lomb) to perform the refractive ablation. As standard practice, a marking pen was used to enable accurate flap realignment. Three weeks after a sudden increase in the incidence of DLK was identified, one of the 5 surgeons performed 5 consecutive bilateral cases using the marking pen in the right eyes but not in the left eyes. RESULTS: Of the 522 LASIK cases (119 without marking pen, 403 with marking pen), DLK developed in 49 (9.4%). No eye treated without the marking pen developed DLK; of those in which the marking pen was used, 49 (12.2%) developed DLK (P < 0.0001, Fischer exact test; odds ratio, 27). In the 5 consecutive bilateral cases in which the marking pen was used in the right eye but not the left eye, 4 right eyes and no left eye developed DLK (P = 0.03). Forty-five of the 49 eyes with DLK quickly recovered. The other 4 developed central toxic keratopathy. CONCLUSION: There is strong statistical evidence that the marking pen was a factor in the occurrence of DLK.