Methods are provided herein for measuring the mutational frequency of a DNA molecule in cells, for example stem cells or hematopoietic cells such as CD34.sup.+ cells or granulocytes. The method includes sequencing corresponding regions of mtDNA from a set of hematopoietic cells, or a set of clonal populations of hematopoietic cells, and comparing the sequence of the corresponding regions of mtDNA from the cells, or clonal populations of cells. The method also includes the comparison of mtDNA sequences with genomic DNA sequences. Also provided are methods for screening for an agent that has a mutagenic effect on a cell. The method includes contacting, or treating, clonal populations of cells with an agent and comparing the sequence of the mtDNA obtained from the treated clonal populations of cells, with the sequence of the corresponding region of mtDNA obtained from a control clonal populations of cells.