An hydrographic section with closely spaced stations (12 nm distance) was performed across the Drake Passage during the DRAKE 2006, ANT-XIII/3 cruise on board RV Polarstern on her way south from Punta Arenas to Jubany station (King-George Island). The section acquired during 16 - 26 January 2006 follows ground track #104 of Jason altimetry satellite. Thus, the section runs parallel to the Shackleton Fracture Zone and crosses the Yaghan Basin and the Ona Basin. The data set comprises the 51 full-depth CTD stations of the south-bound section. The data were obtained with a Sea-Bird Electronics SBE 9/11+ with a 24 Hz sampling frequency. At the end of the cruise, the CTD sensors were sent to Sea-Bird Company for calibration. Conductivity and temperature sensor drifts were negligible (respectively, less than 10–5 S m−1 per year and less than 310–4 K per year). Salinity derived from the CTD measurements was compared with the salinity of samples taken from the water bottles, measured by Guildline-Autosal-8400 salinometer that was adjusted to IAPSO Standard Seawater. The data quality for salinity is better than ±0.002 and for temperature better than ±0.001 K. The data processed with Sea-Bird processing software have a vertical resolution of 0.1 m.