We use serial section scanning probe nanotomography to study the 3D structure, nanoporosity and pore interconnectivity of biocompatible scaffolds made of fibroin and recombinant spidroin 1 (rS1/9). Significant nanoporosity (24%) and pore percolation is detected for rS1/9 scaffolds. It is assumed to contribute to higher in vivo tissue regeneration efficiency of rS1/9 scaffolds.