Background: Cryptococcal meningitis (CM) is an increasingly prevalent infection among HIV/AIDS patients and is becoming a leading cause of morbidity and mortality in Africa. The short-term prognosis and management of patients with CM may be improved by identifying factors leading to mortality in patients with CM. Objective: To assess the clinical management and mortality associated with cryptococcal meningitis (CM) in patients with acquired immunodeficiency syndrome (AIDS) in Kenya. Design: A retrospective study. Setting: Kenyatta National Hospital and Mbagathi District Hospital, between August 2008 and March 2009. Subjects: Seventy six HIV-infected patients confirmed to be CM positive. Results: Results show that 30 (40%) of 76 patients diagnosed with CM died during hospitalisation after a median hospital stay of ten days (range, 2-73 days). Significant predictors of mortality in the univariate model were Mycobacterium tuberculosis (TB) co-infection (P = 0.04), having been diagnosed with a co-morbid condition such as diabetes mellitus, oral candidiasis and hypertension (P = 0.01), and a low median CD4+ T lymphocyte count (P < 0.001). The multivariable model revealed that male sex, previous or current anti-retroviral therapy (ART) at admission and CD4+ T lymphocyte count less than 50 were significant predictors of mortality. Conversely, a minimum of two weeks of amphotericin B treatment (P < 0.001), initiation of ART (P = 0.007) and monitoring of creatinine and electrolyte levels (P = 0.02) were significantly associated with survival in the univariate model. Conclusions: CM-associated mortality in Kenya is high; there is an opportunity to improve the management and the short-term outcomes of hospitalised HIV positive patients with CM in Kenya.