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Trypanosoma brucei has a single nucleus and a single kinetoplast (the mitochondrial genome). Each of these organelles has a distinct S phase, which is followed by a segregation period, prior to cell division. The segregation of the two genomes takes place in a specific temporal order by interaction with microtubule-based structures, the spindle for nuclear DNA and the flagellum basal bodies for the kinetoplast DNA. We used rhizoxin, the anti-microtubule agent and polymerisation inhibitor, or the nuclear DNA synthesis inhibitor aphidicolin, to interfere with cell cycle events in order to study how such events are co-ordinated. We show that T. brucei cytokinesis is not dependent upon either mitosis or nuclear DNA synthesis, suggesting that there are novel cell cycle checkpoints in this organism. Moreover, use of monoclonal antibodies to reveal cytoplasmic events such as basal body duplication shows that some aphidicolin treated cells appear to be in G(1) phase (1K1N) but have activated some cytoplasmic events characteristic of G(2) phase (basal body segregation). We discuss a possible dominant role in trypanosomes for kinetoplast/basal body segregation in control of later cell cycle events such as cytokinesis