Fungal infections continue to cause major complications in cancer patients. With the increasing use of aggressive chemotherapy and stem cell transplantation causing profound, prolonged depressed immunity, the risk of invasive mycoses has increased. The prognosis of these infections is poor unless they are diagnosed and treated promptly. The management of opportunistic fungal infections is characterized by a series of unresolved problems, including initial difficulties in obtaining an early diagnosis. Clinical signs indicating a definite diagnosis of fungal infection is frequently absent in cancer patients. There are no distinctive symptoms and fever is the most common and, frequently, the only sign. In only a minority of cases, and usually after recovery from neutropenia, can some clinical features, such as pulmonary pseudomycetoma and hepatosplenic lesions, be suggestive of an invasive mycosis. Thus, laboratory procedures are necessary to reveal or confirm the diagnosis of invasive mycosis and establish disease etiology. Cultures are often negative and positive results need a careful evaluation to determine clinical importance. The significance of fungi isolated from mucosal surfaces and from the respiratory tract in diagnosing invasive mycoses is controversial. The problem in interpreting these microbiological data is the differentiation between fungal infection and colonization. Detection of fungal antigens by molecular methods appears to be promising, but the significance in various clinical settings is still under evaluation. In most cases, the diagnosis depends on a combination of clinical, microbiological, histological and serological results.