The margin off North-East Greenland between 69°N and 79°N, respectively Scoresby Sund and Boreas Basin, is less well known than the conjugate margin off Norway. The sparse geophysical and geological database of the North-East Greenland margin reveals strong lateral and vertical variations in crustal structure due to the complex rifting history. The crustal structure of the North-East Greenland margin is of special interest for a better understanding of the rifting processes in general, and their variations along the continental margin. Therefore, in summer 2009 deep seismic data were acquired along two profiles in the Norwegian-Greenland Sea: (1) in the Boreas Basin between the Knipovich Ridge and North-East Greenland margin, and (2) in prolongation of an existing crustal transect in the Kong Oscar Fjord (KOF) to the Kolbeinsey Ridge. The two seismic refraction lines show differences in the oceanic crustal structure. At the Knipovich Ridge the crustal thickness is only ~3 km compared to ~10 km at the Kolbeinsey Ridge. The oceanic crustal structure of the Boreas Basin reveals no significant oceanic layer 3 contrasted to normal oceanic structure at the Kolbeinsey Ridge. The upper mantle velocities of the Boreas Basin indicate small lateral variations with an averaged value of 7.5 km/s. In contrast, the upper mantle velocities of oceanic part of the KOF profile emerge considerable lateral variations in range of 7.6-7.9 km/s. These crustal differences indicate northward decreasing of the magmatic influence during the formation of the Norwegian-Greenland Sea.