The aims of this study are i) to screen tumour from patients with leukaemia and lymphoma and determine the incidence of tumour markers, t(14;18) translocation, T-cell receptor δ (TcRδ) chain and immunoglobulin heavy chain (IgH) gene rearrangements ii) to develop sensitive PCR based techniques using these tumour markers and iii) to analyse serial remission samples and peripheral blood stem cells (PBSC) for residual tumour. Southern bolt analysis showed that 55% of patients with pre-B acute lymphoblastic leukaemia (ALL) had TcR Vδ2-Dδ3 rearrangements and that 85% of patients with B-lineage disease had IgH rearrangements. PCR analysis showed a TcRδ marker in 53% of pre B ALL and a CDRIII marker in 77% of B-lineage disorders therefore these patients were available for further study of minimal disease. Direct sequence analysis of PCR products from TcR Vδ2-Dδ3 and the third complementarity-determining region (CDRIII) of IgH demonstrated sufficient junctional diversity to permit unique clone specific probes of 20 nucleotides to be designed. Junctional diversity was generated by random N- nucleotide insertion, gene segment deletion and addition of other D segments.