Individual fungal cells within genetically-uniform populations can exhibit striking phenotypic variability. This phenotypic heterogeneity has been proposed recently to promote the fitness of fungal populations, independently of fitness contributions arising from genetic diversity. Consequently, several major recent studies have been focused on unravelling the physiological and molecular bases for heterogeneity. This article provides an overview of the current state of play in this emerging field, with a focus on heterogeneity in the single-cell yeast Saccharomyces cerevisiae and on the novel methodologies being developed to study heterogeneity.