The investigation of presumed microbial keratitis includes microscopy and culture of corneal specimens obtained by scraping the infiltrated cornea. Routine microscopy fails to identify the infecting organism in about 15% of cases. We discuss the problems presented by 20 such eyes which required further investigation. We present a diagnostic algorithm aimed at reducing the delay in identifying the pathogen and increasing the rate of positive culture. This is important since unusual pathogens may require treatment with drugs other than the 'first line' broad spectrum combination of an aminoglycoside and a cephalosporin. The algorithm allows sequential restaining and reculturing of specimens for more thorough investigation. In addition to the use of special stains and culture conditions, it presents indications for further corneal scrapes and biopsies. Uncontrolled infection resulted in five perforations and penetrating keratoplasty was indicated in 11 cases. The visual outcome for these patients was poor with fewer than 30% achieving 6/12 acuity. The delay in diagnosis increases morbidity and this should be significantly reduced by adopting the algorithm we propose.