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We present an extensive study of the underlying structure of femtosecond laser-induced nanogratings in fused silica. To explore the evolution of the three-dimensional structure of the nanopores and cracks, of which the nanogratings consist, we performed small angle X-ray scattering measurements as well as focused ion beam milling and scanning electron microscopy. Our results show that cracks with dimensions of (280
×
25
×
380) nm
3
and nanopores with typical diameters of (30
×
25
×
75) nm
3
are formed independent of various illumination parameters. With increasing number of laser pulses the smaller pores fuse to larger structures. Furthermore, the data suggest a cross-sectional change of the pores from cuboidal to ellipsoidal.