Molecular analysis of clinical samples has been hampered by the lack of fresh or frozen specimens and the presence of contaminating background cells within samples obscuring the molecular analysis of the pathological cells of interest. Routine cytology specimens are a ubiquitous and abundant, yet largely untapped, source of clinical samples for molecular analysis. Morphologically defined single cells from peripheral blood smears can be microdissected from contaminating background cells and their whole genome amplified by primer extension preamplification, followed by polymerase chain reaction analysis of the specific DNA of interest. Thus, molecular information can be traced back to the cell of origin in these clinical specimens. This should allow studies on clonality, loss of heterozygosity, mutation, or amplification of multiple loci from one single cell in haematological smears and possibly other clinical cytology specimens.