The invention provides methods for the identification of members of a malignant lymphocyte clone by analysis of clonotypic DNA rearrangements of T cell or B cell receptor genes. The DNA or RNA from isolated single tumor cells is amplified by PCR using consensus primers to the VDJ region of the receptor genes, and the sequence of the VDJ region is obtained from each. The clonotypic sequence of the malignant clone is identified as the most frequent VDJ sequence amplified. Individual-specific PCR primers for the VDJ region are then designed based upon the clonotypic sequence. These specific PCR primers are used to detect and quantitate clonotypic cells in subsequent patient samples using in situ PCR or in situ RT-PCR. Fractionated or unfractionated samples of blood or bone marrow, as well as tissue sections can be analyzed. The methods provide a highly sensitive and quantitative means to monitor the progress of disease and the efficacy of treatment protocols, as well as to detect members of the malignant clone in autologous bone marrow cells destined for transplant.