Hospital sterile service departments (SSDs) currently rely on simple visual confirmation of cleanliness as an assessment of the efficacy of cleaning surgical instruments. The inherent inability to monitor low levels of infectious or proteinaceous contamination on surgical instruments creates the possibility that highly dangerous and robust biological agents may remain infectious and undetected even after standard cleaning and sterilization procedures have been employed. This paper describes the development of a novel microscopy technique, episcopic differential interference contrast microscope, combined with the fluorescent reagent, SYPRO Ruby, to rapidly detect brain tissue protein to below 400 pg/mm(2) on an instrument surface. This technique has displayed a minimum level of detection observed by 50% of volunteers of 85 pg/mm(2) (95% confidence intervals 67-112 pg/mm(2)). Quantitative assessment of instruments supplied from various SSDs enabled the establishment of a 'contamination index' of both proteinaceous and non-proteinaceous deposits on the surface. This new methodology for the assessment of surface contamination is generally applicable and should facilitate future quantitative surveys of instrument contamination in hospitals and other healthcare environments.