Between 2005 and 2008, the prevalence of systemic mycosis among 1,300 HIV/AIDS patients in Cuiabá, Mato Grosso, was 4.6%. The fungus species isolated were Cryptococcus neoformans in 50%, Cryptococcus gattii in 1.6%, Cryptococcus spp in 6.6%, Histoplasma capsulatum in 38.3% and Paracoccidioides brasiliensis in 3.3%. Death was recorded in the cases of 32 patients (53.3%), and cryptococcosis was the main cause. The CD4+ T lymphocyte count was low and similar among patients who survived or died due to systemic mycosis. The factors independently associated with the deaths of these patients were alcoholism (OR: 8.2; 95% CI: 1.4-62.1; p = 0005) and the mean level of lactate dehydrogenase [758 (182) U/l vs. 416 (268) U/l; p < 0001]. The findings showed that systemic mycosis was highly lethal among the patients with HIV/AIDS in Cuiabá and suggested that clinical-laboratory characteristics such as alcoholism and early elevation of lactate dehydrogenase may be factors relating to worse prognosis under these conditions.