The deep structure of the southern Apennines (SA) accretionary wedge is still debated since industrial seismic reflection and well data provide reliable constraints only to a depth of about 10 km. As a consequence, two directly linked questions regard (1) the shortening in the accretionary prism (particularly within the buried Apulian thrust units) and (2) the degree of involvement of the lower plate basement (i.e., the Apulian crystalline basement). To address these issues, we have constructed a regional section along a recently released deep seismic reflection profile (CROP-04) which intersects the entire SA. The resulting cross section, adequately constrained to a depth of about 15 km, has been framed in a geodynamic scenario characterized by the eastward roll-back of the westward subducting Apulo-Adriatic lithosphere. On the basis of this section we speculate on the deep structure, building both thin- and thick-skinned thrust models. A cross-check of these end-members models against documented tectonic, geophysical, and geochemical features shows that the thin-skinned model is generally more consistent with the available data. The development of basement slices with thicknesses of tens of kilometers is unlikely, while it remains possible that the Apulian basement could have been involved with its upper few kilometers. In the thin-skinned model, the total shortening of the allochthonous units (i.e., Apennine and Apulian carbonate platforms and Lagonegro basin) is estimated to be greater than 280--300 km. Some 90 km of shortening can be attributed to the Apulian thrust units.