Corneal collagen cross-linking (CCL) is a treatment modality that has been shown to stop the progression of keratoconus. There have also been reports that CCL acts as an antimicrobiologic agent in treating resistant microbial keratitis. This study aimed to investigate the agents of bacterial contamination of contact lenses after CCL, correlate the microbiologic findings to clinical data, and present the possible changes to the ocular flora after riboflavin / UVA. Sixty-three patients underwent CCL for keratoconus, while the control group had 41 patients having photorefractive keratectomy (PRK) for high myopia. Both procedures were carried out according to standard protocols. At the end of both procedures the cornea was irrigated with a chilled balanced salt solution, and a drop of moxifloxacin instilled onto the cornea. Finally a bandage contact lens (BCL) was inserted at the end of both procedures. Topical moxifloxacin and Refresh tear drops were used every two hours postoperatively until epithelial closure, at which point the BCL was removed and placed into brain-heart infusion agar. After 48 hours of incubation, samples of both were added to blood agar, chocolate agar and eosin methylene blue agar plates. Samples were accepted to be positive if one or more colony-forming units were shown. There were positive cultures in 12 (16.7%) of the lenses in the CCL group and five (12.2%) in the PRK group. In the CCL group, 10 grew coagulase negative staphylococci (CNS), one grew alpha haemolytic streptococci and one grew diphteroid spp. In the PRK group, CNS was isolated from four lenses and diphteroid spp from one contact lens. There was no statistical difference between the control and corneal collagen cross-linking groups for bacterial colonisation (p=0.523), and all isolated microorganisms were susceptible to the administered topical antibiotic (moxifloxacin). Suggested reasons for the higher contamination rate in the CCL group include longer duration of BCL wear and longer duration of ocular surface exposure. All the isolated bacteria were sensitive to moxifloxacin. The contact lens cultures showed similar bacterial results in both groups, and these outcomes suggest that the ocular flora is not changed after CCL.