Flavopiridol, a synthetic flavone, is currently under clinical investigation for the treatment of B‐cell chronic lymphocytic leukaemia (B‐CLL). In this study, we examined the in vitro effects of flavopiridol and fludarabine on B‐CLL cells from 64 patients (36 treated and 28 untreated) in terms of apoptosis induction and Bcl‐2 family expression. Both flavopiridol and fludarabine induced apoptosis in all the samples tested with mean LD₅₀ values (± SD) of 59·7 nmol/l (± 36·5) and 6·2 μmol/l (± 7·5) respectively. Mean flavopiridol LD₅₀ values were not significantly different between the treated and untreated patient groups (P = 0·35), whereas the fludarabine LD₅₀ values were significantly higher in the previously treated patient group (P = 0·01). Bcl‐2 and Mcl‐1 expression were downregulated in both flavopiridol and fludarabine‐induced apoptotic cells, but the increase in Bax expression that accompanied fludarabine‐induced apoptosis was not evident in flavopiridol‐treated cells. In addition, Bcl‐2:Bax ratios were not predictive of flavopiridol cytotoxicity (P = 0·82), whereas they were highly predictive of in vitro responsiveness to fludarabine (P = 0·001). Overall, these findings suggest that flavopiridol exerts its cytotoxic effect through a novel cell‐death pathway that is not subject to the Bcl‐2 family mediated resistance mechanisms that reduce the efficacy of many conventional chemotherapeutic drugs.