A comprehensive study of the occurrence of two-shell clusters with the first shell as a Frank-Kasper polyhedron Z12, Z14, Z15, or Z16 (Frank-Kasper nanoclusters) is performed for 22 951 crystal structures of intermetallics containing only metal atoms. It is shown that besides the familiar Bergman and Mackay clusters, two more types of high-symmetrical icosahedron-based nanoclusters are rather frequent; they both have a 50-atom second shell. Moreover, two types of high-symmetrical Frank-Kasper nanoclusters with a Friauf-polyhedron (Z16) core are revealed; these nanoclusters have 44 and 58 atoms in the second shell. On the contrary, Z14 and Z15 Frank-Kasper polyhedra have been found to be rare and improper to form distinct nanoclusters in crystals. The second shells of Frank-Kasper nanoclusters have been revealed possessing their own stability: they can be realized in nanoclusters with different internal polyhedra and can shift around the core shell. The role of Frank-Kasper nanoclusters in assembling intermetallic crystal structures is illustrated by several examples.