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Two cases of cryptococcal meningitis went undetected by a cryptococcal antigen (CrAg) lateral flow assay on blood in a reflex CrAg screen-and-treat programme in South Africa, although <i>Cryptococcus neoformans</i> was identified by culturing the cerebrospinal fluid specimens. Further investigations into these discordant diagnostic results included multilocus sequence typing (which showed no mutations in the CAP59 gene) and transmission electron microscopy using a capsule-staining protocol (which revealed a &gt;50% reduction in capsular material in both cases, relative to a control culture). A multi-disciplinary approach for resolving discordant diagnostic test results is recommended.