Abstract The detection and quantification of cryptococcal capsular PS antigen in body fluids is useful for the diagnosis of cryptococcosis. We compared the sensitivity of four assays for measuring amount of cryptococcal PS and two clinical assays (lateral flow assay (LFA) (IMMY) and the cryptococcal latex agglutination assay (CLAA) (Remel)) using the PS of four single motif repeat expressing Cryptococcus strains. These showed relatively consistent laboratory assay inter-strain sensitivity with significant inter-strain variation with the more sensitive clinical assays showing variation consistent with antigenic differences. Analysis of LFA false-negative isolates reveals cryptococcal PS motif expression is not recognized by the antibodies used in the assay. These results suggest that strain variation in PS structure affects the sensitivity of the various quantification tests while antigen-antibody matching is essential to avoid false negative results in cryptococcal antigen testing of bodily fluids. Including antibodies with more specificities in clinical assays could reduce false-negative results.