Three-dimensional modeling of data from 31 vertical electrical and 24 magnetotelluric soundings collected in the Baringo-Bogoria Basin (central Kenya Rift Valley) shows a thick succession of well-defined tectonostratigraphic units beneath the Recent deposits of the Marigat-Loboi Plain. They include from top to bottom, a sedimentary basin, ∼1.5 km thick, controlled by N-S and N140° structural trends, and a thick homogeneous resistive layer related to the bottom of the basin, overlying a conductive structure, which cannot be clearly correlated with the Proterozoic basement. It is suggested that the resistive layer correlates with the mid-Miocene plateau-type flood phonolites which flowed over the early Kenya Rift during a major volcanic activity period. The conductive structure overlain by these lava flows could be a sedimentary basin developed during the initial phase of rifting, during the Oligocene-Miocene. The absence of a significant gravity low associated with this deep basin suggests a zone of dense intrusion deeper than 5–10 km, not discernible with the magnetotelluric data but required to explain the gravity anomalies. The recognition of a deeply buried sedimentary succession lying between 4 and 8 km beneath the lower Miocene volcanic series of the Baringo valley would provide new insights into the regional volcano-sedimentary stratigraphie succession and the rift development of the Kerio and Baringo Basins.