The regional contribution to the geo-neutrino signal at Gran Sasso National Laboratory (LNGS) was determined based on a detailed geological, geochemical and geophysical study of the region. U and Th abundances of more than 50 samples representative of the main lithotypes belonging to the Mesozoic and Cenozoic sedimentary cover were analyzed. Sedimentary rocks were grouped into four main " reservoirs" based on similar depositional settings and mineralogy. The initial assumption that similar chemico-physical depositional conditions would lead to comparable U and Th contents, was then confirmed by chemical analyses. Basement rocks do not outcrop in the area. Thus U and Th in the upper and lower crust of Valsugana and Ivrea-Verbano areas were analyzed. Irrespective of magmatic or metamorphic origin lithotypes were subdivided into a mafic and an acid reservoir, with comparable U and Th abundances.Based on geological and geophysical properties, relative abundances of the various reservoirs were calculated and used to obtain the weighted U and Th abundances for each of the three geological layers (sedimentary cover, upper and lower crust). Using the available seismic profile as well as the stratigraphic records from a number of exploration wells, a 3D modeling was developed over an area of 2°×2° down to the Moho depth, for a total volume of about 1.2×106km3. This model allowed us to determine the volume of the various geological layers and eventually integrate the Th and U contents of the whole crust beneath LNGS.On this base the local contribution to the geo-neutrino flux (S) was calculated and added to the contribution given by the rest of the world, yielding a refined reference model prediction for the geo-neutrino signal in the Borexino detector at LNGS: S(U) = (28.7 ± 3.9) TNU and S(Th) = (7.5 ± 1.0) TNU. An excess over the total flux of about 4 TNU was previously obtained by Mantovani et al. (2004) who calculated, based on general worldwide assumptions, a signal of 40.5 TNU. The considerable thickness of the sedimentary rocks, almost predominantly represented by U- and Th-poor carbonatic rocks in the area near LNGS, is responsible for this difference. Thus the need for detailed integrated geological study is underlined by this work, if the usefulness of the geo-neutrino flux for characterizing the global U and Th distribution within the Earth's crust, mantle and core is to be realized.