Corneal transplantation is undergoing significant change because the dysfunctional portion of the cornea may now be selectively transplanted. After recovery of corneoscleral tissue, further processing of such tissue as in microkeratome preparation of endothelial keratoplasty lenticules is defined as “open-container processing” by the Eye Bank Association of America. Airborne bacterial contamination during preparation of corneal tissue is a potential source of postoperative infection. This review addresses ways to minimize the risk of disease transmission as corneal tissue is processed for lamellar keratoplasty, endothelial keratoplasty, or femtosecond laser-assisted penetrating keratoplasty and to minimize risk to eye bank personnel or physicians preparing the tissue. Secondly, quality assurance measures are described that qualify the environment in which corneal tissue is being processed. We propose that the environment in which corneal tissue is being processed must be able to demonstrate acceptable levels of airborne microbial contamination annually as measured by settle plates to estimate airborne bacterial sedimentation. It is recommended that any environment where corneal tissue is prepared should meet the minimum standard of a conventional operating room which is <25 colony-forming unit per 90-mm settle plate per 1-hour exposure.