The effectiveness of surface sterilization methods were compared using root tissue of barley (Hordeum vulgare) colonized by two Chaetomium species in an aseptic plant growth system. The reliability of different sterilants to inhibit ascospore germination was tested. Ascospores on nitrocellulose membranes were either treated directly or ascospores adhering to axenic barley seedlings were treated on plant tissue. Inhibition of ascospore germination on nitrocellulose membranes was achieved with lower concentrations of sterilants than when the spores were on plant surfaces. A 10% peracetic acid treatment was necessary if experiments were conducted ad planta. The sterilants penetrated into epidermal root tissue and caused damage to this area, as shown by the vital dye DiOC7(3). It was concluded that effective surface sterilization techniques for ascospores adhering superficially to plant tissue were not appropriate for the detection of fungi growing within the epidermis.