Updated project metadata. The most common cause of cryptococcal meningitis is Cryptococcus neoformans. The addition of 5-fluorocytosine to the treatment of patient with this potentially fatal infection significantly improves disease outcome. However, developing resistance to this drug is a serious problem in patient management. In this study, we investigated the molecular mechanisms causing 5-FC resistance in three clinical isolates of C. neoformans using genomic and proteomic approaches. Our findings show that genetic alterations in genes involved in the pyrimidine salvage pathway caused 5-FC resistance in these isolates. Specifically, one isolate had a missense mutation (E64G) in the uracil phosphoribosyl transferase gene (FUR1), another isolate had a large deletion spanning the cytosine deaminase gene (FCY1), and the third isolate had a point mutation in the same gene leading to a truncated protein at amino acid 164 (STOPW164*). Proteomic data confirmed that the genetic changes led to the absence or decreased the amount of the enzymes in the 5-FC resistant isolates. Transformation experiments confirmed that the genetic changes ultimately affected 5-FC susceptibility, providing further evidence of the effect of the genetic changes on 5-FC susceptibility.