Corneal laser refractive surgery is increasingly being performed on patients with the aim of improving unaided vision. Most candidates for surgery have excellent spectacle- or contact lens-corrected vision. Although microbial keratitis following refractive surgery is a rare complication, and usually has a good visual outcome, it can be sight-threatening. The spectrum of pathogens differs to other causes of microbial keratitis, such as contact lens-associated keratitis, and a different management approach is required. Postoperatively, patients are prescribed topical steroids and broad-spectrum topical antibiotics, typically fluoroquinolones. These do not cover unusual organisms, such as fungi, Nocardia, Acanthamoeba and some atypical mycobacteria. In post-laser-assisted in situ keratomileusis microbial keratitis, the lamellar flap should be lifted to acquire samples for specific microbiological examination, including these atypical organisms. Confocal microscopy is a noninvasive test that provides morphological information, and is operator dependent, but may assist in the rapid diagnosis of fungal, Acanthamoeba or Norcardia keratitis. PCR is not in widespread use, but has high sensitivity and specificity, and may facilitate early diagnosis and specific treatment of the causative organism, which is critical in obtaining the best clinical outcome.