The control of gene expression by rearrangement of DNA sequences, in prokaryotes and eukaryotes, is recorded in several instances. These accompany the differentiation of cells, yielding a new phenotype. The possibility of such a means of gene control operating in Physarum was considered; this organism undergoes marked changes in cell morphology and function during the amoebal-plasmodial transition. Genes activated or inactivated in this transition were examined for possible changes in structure. This was done by using amoebal- and plasmodial-specific cDNAs to probe Southern blots of amoebal and plasmodial DNA, digested with restriction endonucleases. This procedure should have revealed any restriction enzyme polymorphisms that might have existed between amoebae and plasmodia as a result of DNA rearrangements. However, no changes in DNA structure were observed between amoebae and plasmodia. The scope of this investigation is critically assessed. The methylation of cytosine residues has also been proposed as a means of controlling gene expression in eukaryotes. The available amoebal- and plasmodial-specific cDNAs were used therefore to probe Southern blots of amoebal and plasmodial DNA digested with methylation sensitive and insensitive restriction enzymes, in order to examine the methylation patterns of DNA from the two forms. For all phase-specific genes tested, the patterns in amoebae and plasmodia were identical, suggesting that no changes had occurred. Again, the scope of this investigation is assessed, and the possibility of a more extensive search for putative DNA rearrangements or changes in methylation pattern is mooted. To study closely the structure of three plasmodial-specific genes, attempts were made to clone regions of Physarum genomic DNA containing these sequences. It was not possible to isolate positive clones in any useful quantity. The probable reasons for the difficulties encountered are discussed.