Deep seismic profiling of the Amazonian craton (northern Brazil) reveals previously unknown deep structural features buried beneath a thin, relatively flat Phanerozoic sedimentary cover (Amazon basin). The seismic signature of the Precambrian crust is characterized by a transparent shallow basement down to 8–9 km followed by a highly reflective middle and lower crust. Middle and lower crustal events are dominated by abundant dipping, asymmetric arcuate reflections and diffractions, the shallowest of which occur beneath a structural arch (Jutaí arch). Although wide angle refraction data are unavailable, a decrease in the number of coherent reflections at about 15 s two‐way travel time (45 km) and small drops in amplitude and increases in average frequency are interpreted to mark the Moho. The deep Amazonian seismic line is located near the westernmost boundary of the Amazonian craton, imaging the Rondonian province, one of the youngest geochronological provinces of the craton (middle Proterozoic). To the south, the Rondonian basement crops out, revealing schists, gneisses, granulites, and important volumes of anorogenic granites. The prominent, laterally extensive arcuate reflections observed within the middle and lower crust may be related to this anorogenic magmatic activity, perhaps corresponding to layered intrusive complexes. On the other hand, intrusion of mantle derived material during an early Paleozoic rifting, as well as the Mesozoic episodes of mafic intrusion may also have contributed to this seismic signature. Similar seismic signatures found in eastern Australia and on COCORP profiles of the central U.S. craton suggest that such cratonic terranes may have undergone similar tectonic evolution. In the upper crust, probable fault plane reflections associated with ENE‐WSW reverse faults of Jurassic‐Early Cretaceous age may sole into the top of the reflective zone, suggesting that the lower limit of the transparent upper crust may represent a rheological boundary.