Abstract Criticism of the use of chromosomal puffing in dipteran polytene nuclei as an indicator of gene activity is examined in relation to the selection of experimental systems and the presumed range of synthetic activities carried out by each type of cell. A major criterion of selection has been the favourability of Chromosome morphology for cytological analysis. As a consequence, the proportion of the genome which may become activated in a range of functionally diverse cells appears to have been under-estimated. Comparative aspects of polytene chromosome behaviour in different tissues and at different stages of development are illustrated with reference to footpad and trichogen cells from pupae, and to salivary grand and fat body cells from larvae, of the brown blowfly, Calliphora stygia. Other problems of interpretation arising in studies of chromosomal puffing are briefly reviewed.