Abstract Assessment of the underground geothermal potential requires the knowledge of deep temperatures (1–5 km). Here, we present new temperature maps obtained from oil boreholes in the French sedimentary basins. Because of their origin, the data need to be corrected, and their local character necessitates spatial interpolation. Previous maps were obtained in the 1970s using empirical corrections and manual interpolation. In this study, we update the number of measurements by using values collected during the last thirty years, correct the temperatures for transient perturbations and carry out statistical analyses before modelling the 3D distribution of temperatures. This dataset provides 977 temperatures corrected for transient perturbations in 593 boreholes located in the French sedimentary basins. An average temperature gradient of 30.6°C/km is obtained for a representative surface temperature of 10°C. When surface temperature is not accounted for, deep measurements are best fitted with a temperature gradient of 25.7°C/km. We perform a geostatistical analysis on a residual temperature dataset (using a drift of 25.7°C/km) to constrain the 3D interpolation kriging procedure with horizontal and vertical models of variograms. The interpolated residual temperatures are added to the country-scale averaged drift in order to get a three dimensional thermal structure of the French sedimentary basins. The 3D thermal block enables us to extract isothermal surfaces and 2D sections (iso-depth maps and iso-longitude cross-sections). A number of anomalies with a limited depth and spatial extension have been identified, from shallow in the Rhine graben and Aquitanian basin, to deep in the Provence basin. Some of these anomalies (Paris basin, Alsace, south of the Provence basin) may be partly related to thick insulating sediments, while for some others (southwestern Aquitanian basin, part of the Provence basin) large-scale fluid circulation may explain superimposed cold and warm anomalies.