Controlled source audio-magnetotelluric (CSAMT) has been used to investigate the resistivity structure of the summit region of Karthala volcano. The major purpose of this CSAMT survey is to locate the active hydrothermal system. The presence of the hydrothermal system had already been inferred from surface evidence of hydrothermal activity and from self-potential (SP) mapping of the Karthala summit zone. The results of the 1D CSAMT inversion indicate the following: (1) a highly resistive (500–5000 Ω m) 200- to 400-m thick surface layer, that is characteristic of dry basaltic rocks, and made up of lava flows and/or tuff breccias; (2) a 300- to 1200-m thick layer of intermediate resistivity (20–400 Ω m), thought to be representative of the groundwater body; and (3) a deep conductor with a resistivity of less than 2 Ω m, which might be related to the active hydrothermal system. This hydrothermal system appears to be bounded by caldera edges and shows the same north–south trend. Its depth ranges from more than 1 km to less than 0.7 km in the northern part of the caldera and its resistivity ranges from 2 to 0.5 Ω m in the northern part of the caldera. Less resistive zones and the shallowest depths of this conductive layer are well correlated with the largest SP positive anomalies and are assumed to be generated by hot fluid circulation. The most active hydrothermal zone is situated in the northern part of the caldera.