The bimodal Naivasha complex (central Kenya) comprises 2 suites of transitional basalts and 7 chemostratigraphic groups of comendites. The early basalt series (EBS) predates the Group 1 comendites with the later series (LBS) erupted between Groups 5 and 6. Basalts from both suites are notable for their relatively radiogenic 207Pb/204Pb isotope ratios which are higher than in the majority of ocean island basalt (OIB, Zindler & Hart, 1986), and 87Sr/86Sr ratios more radiogenic than basalts from northern Kenya. Both basalt suites exhibit systematic trace element and isotopic variations which appear related to greater assimilation of Proterozoic amphibolite facies crust by the chemically more evolved rock types. Their mantle source regions show evidence of residual plagioclase and have a 'Dupal'-like OIB trace element and Pb-Sr-Nd isotope signature (Hart, 1984). A contribution from the sub-continental lithosphere is proposed in basalt genesis.The seven comendite groups have distinct trace element and isotope systematics. Hydration of comendite glass causes significant changes in Sr and Pb isotope ratios. In terms of their Sr-Nd isotope relationships the unaltered comendites could be derived from the basalts by an assimilation-fractional crystallization (AFC) process dominated by the fractional crystallization of feldspars. However, the Pb systematics clearly demonstrate that the basalts and comendites are not part of a cogenetic suite. Chemical variations within individual comendite groups are predominantly the result of fractional crystallization of the observed phenocryst assemblages (i.e. alkali feldspar dominated) and minor crustal interaction. The majority of the chemical and isotopic differences between Groups 1-7 cannot be explained by fractional crystallization and appear to represent crustal melts derived from close to the interface between Pan African basement and the overlying Miocene-Holocene volcanoclastic rocks, at approximately 6 km depth (KRISP working group, 1987).Halogens play a fundamental role in the petrogenesis of the comendites (Cl+F<1·7 per cent) permitting small degree melts of low viscosity to be extracted from the crust and causing the breakdown of minor phases e.g, zircon. These factors explain the extreme enrichment of certain incompatible trace elements (Zr<2500, Nb<700) in the comendites and coupled with the retention of zircon in the source of the halogen poor comendites (Group 1<0·6 per cent Cl+F) result in notable fractionation among the HFSE (Zr/Nb 1·5-5·5). Halogens may be concentrated in the source region from the surrounding crust by the presently active hydrothermal system. Each of the chemostratigraphic comendite groups is chemically distinct, implying that partial melting of the heterogeneous crust is on a limited scale and that no extensive magma chambers exist beneath Naivasha.