We have adapted a system for in vitro differentiation of a monomorphic trypanosome strain to monitor changes in transcription and DNA modification in expression sites during the transition of the bloodstream-form to the procyclic trypanosome. We have used trypanosomes that have a gene for drug resistance integrated in an expression site, just downstream of either an expression site promoter, or a ribosomal promoter replacing the endogenous promoter. During the transition from bloodstream-form to procyclic, the promoters in an active expression site behave as expected on the basis of previous work on these promoters in procyclics, i.e. the ribosomal replacement promoter remains fully active, whereas the expression site promoter is (incompletely) down-regulated. A silent bloodstream-form expression site promoter does not remain tightly silenced, however. There is a transient increase of transcription of the marker gene during the transition from bloodstream-form to procyclic, indicating that the control of silent expression sites differs between the bloodstream-form and the procyclic trypanosome, and that a short time is required to reset the silencing mechanisms. One of the differences between bloodstream-form and procyclic trypanosomes is the presence of the modified base beta-D-glucosyl-hydroxymethyluracil (J) in and around bloodstream-form expression sites. We have studied loss of this DNA modification and find that the change in expression site control from bloodstream-form to procyclic does not require active removal of J. Base J is lost by synthesis of new, unmodified DNA, which happens after the major changes in expression site transcription have occurred.