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Phenotypic cell-to-cell variability within clonal populations may be a manifestation of ‘gene expression noise’^,,,,,, or it may reflect stable phenotypic variants. Such ‘non-genetic cell individuality’ can arise from the slow fluctuations of protein levels in mammalian cells. These fluctuations produce persistent cell individuality, thereby rendering a clonal population heterogeneous. However, it remains unknown whether this heterogeneity may account for the stochasticity of cell fate decisions in stem cells. Here we show that in clonal populations of mouse haematopoietic progenitor cells, spontaneous ‘outlier’ cells with either extremely high or low expression levels of the stem cell marker Sca-1 (also known as Ly6a; ref. ) reconstitute the parental distribution of Sca-1 but do so only after more than one week. This slow relaxation is described by a gaussian mixture model that incorporates noise-driven transitions between …