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 PdnL2n2n complexes was prepared by mixing six different dipyridyl ligands with substoichiometric amounts of Pd(CH3CN)42. Analysis of the equilibrated reaction mixture revealed the preferential formation of a heteroleptic Pd6L6L′612 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′612 cage was obtained by using metalloligands instead of organic dipyridyl ligands.