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New Pb isotopic data are presented for 10 young Mesozoic to Cenozoic (0–116 Ma) carbonatites from a 1400 km long segment of the East African Rift. Patterns observed in Pb vs Pb, Sr vs Pb and Nd vs Pb isotope diagrams define unusual, nearly linear, trends that are interpreted as mixing between two components that are broadly similar to the two mantle end-member components, HIMU and EM1, which were first recognized from ocean-island basalts. The two plutons with isotope signatures closest to HIMU and EM1 crop out within 140 km of each other. From these data, EM1 and HIMU are now known to occur in both continental and oceanic settings that are associated with plumes or rifts. Moreover, these isotopic signatures tend to occur in regions where seismic tomography indicates prominent low-velocity zones in the lower mantle. For these reasons, we favour a model for the origin of the East African Rift carbonatites that involves melting and mixing of HIMU and EM1 components contained within an isotopically heterogeneous mantle plume. We consider the HIMU and EM1 sources to be stored within the deep (lower 1000 km) mantle, possibly the core–mantle boundary. The role that continental lithosphere plays in carbonatite generation is probably one of concentrating volatiles at the upper levels of an ascending mantle plume. [ABSTRACT FROM PUBLISHER]