Aim. To perform a study of three-dimensional micro- and nanostructure of porous biocompatible scaffolds and quantitative analysis of nanoscale porosity parameters. Materials and methods . Three-dimensional porous scaffolds made from spidroin rS1/9 (recombinant analog of spider dragline protein) were produced by salt leaching technique. Dimensions of macropores in produced three-imensional scaffolds were in range from 200 to 400 microns. The study of three-dimensional structure of scaffolds was carried out by scanning probe nanotomography technique with the use of experimental setup combining ultramicrotome and scanning probe microscope. Results. Three-dimensional nanotomographical reconstruction of scaffold macropore wall structure is obtained. The formation of three-dimensional network of interconnected pores and channels with characteristic dimensions in range from 20 to 700 nm in the volume of macropore walls of studied scaffolds is observed. Mean pore diameter is 150 nm. Volume porosity of macropore walls is 22% while volume fraction of pores interconnected in large pore clusters is about 20% of all pore volume. Conclusion. Obtained as a result of the study quantitative characteristics of porous micro- and nanostructure of scaffolds show signifi cant degree of nanoscale porosity and percolation of macropore walls what correlates with reported high effi ciency of tissue regeneration on such scaffolds implanted in vivo. Use of scanning probe nanotomography technique for analysis of characteristics and topology of micro- and nanopore systems enables to improve effi ciency of development of novel biocompatible and biodegradable materials with predicted morphological, physical, chemical and biological characteristics.