Perforin-like proteins are pore-forming proteins that function as key immune effectors in the mammalian immune system. Typically, these molecules bind membranes and oligomerise to form large pores that are heterogeneous in size and shape. The latter properties of the pore thus present considerable challenges for structure determination using X-ray crystallography. Here we present the sub-nanometer EM structure of a perforin-like protein, together with the X-ray crystal structure of a second perforin-like protein in a pre-pore-like dimeric form.