The design of structurally defined heteroleptic coordination cages is a challenging task, and only few examples are known to date. Here we describe a selection approach that allowed the identification of a novel hexanuclear Pd cage containing two types of dipyridyl ligands. A virtual combinatorial library of [PdnL2n](BF4)2n complexes was prepared by mixing six different dipyridyl ligands with substoichiometric amounts of [Pd(CH3CN)4](BF4)2. Analysis of the equilibrated reaction mixture revealed the preferential formation of a heteroleptic [Pd6L6L′6](BF4)12 assembly. The complex was prepared on a preparative scale by a targeted synthesis, and its structure was elucidated by single-crystal X-ray diffraction. It features an unprecedented trigonal-antiprismatic cage structure with two triangular Pd3L3 macrocycles bridged by six L′ ligands. A related but significantly larger [Pd6L6L′6](BF4)12 cage was obtained by using metalloligands instead of organic dipyridyl ligands.