Many Histoplasma capsulatum strains spontaneously give rise to variants during broth culture or subsequent to ingestion by epithelial cells. Unlike their parents, these variants are defective in killing macrophages and lack a major cell wall constituent, alpha-(1,3)-glucan. Inside macrophages, where the variants can persist for several weeks, they adopted an unusual morphology strikingly similar to that reported in the tissues of persistently infected humans or animals. These yeasts were often enlarged or misshapen (allomorphic), but were viable. Decreased cytotoxicity for macrophages was more strongly associated with allomorph formation than was the absence of cell wall alpha-(1,3)-glucan. Allomorphs were also formed in rat and mouse resident macrophages, but not in hamster trachea epithelial cells, indicating that host cell type influences the morphology of these yeasts. We propose that during H. capsulatum infection of mammalian hosts, spontaneous variants arise which can be recognized by their unusual morphologies. In contrast with their virulent parents, such variants "peacefully coexist" within macrophages, potentially contributing to the establishment of latency in vivo.