The apo(a) component of Lp(a) plays a major role in mediating the pathological effects of Lp(a) in vascular disease. Apo(a) is composed of repeating kringle (K) domains, of which 10 types are unique (KIV1; KIV3-KIV10; KV) and one (KIV2) is present in variable numbers. KIV7 and KIV8 contain weak lysine binding sites (LBS) that play a role in Lp(a) assembly and KIV10 contains a strong LBS important for binding of Lp(a) to biological substrates and the attachment of pro-inflammatory oxidized phospholipids. Following the kringle domains is an inactive protease domain. While the structures of individual kringles have been solved, no structural information exists on intact apo(a). We therefore performed in silico molecular modeling of apo(a) KIV7-protease. This region contains the key functional domains of apo(a) and has a similar topology to plasminogen. The structures of human, rhesus monkey (lacking the KIV10 strong LBS) and baboon (lacking KV) apo(a) were modeled with Swiss-Model using the crystal structure of the closed conformation of full-length plasminogen (pdb: 4A5T) as the template, followed by energy minimization using Rosetta Relax. The lowest energy human apo(a) model represented a compact, plasminogen-like, tertiary structure that promoted high solvent exposure of the KIV7 LBS and the KIV9 unpaired cysteine, moderate exposure of the KIV10 LBS, and low exposure of the KIV8 LBS. Interestingly, there was substantial variability in the energy minimized models; of the 10 lowest energy models from Rosetta Relax, two showed notable translation of the protease domain resulting in increased solvent exposure of KIV8 at the expense of KIV10. The rhesus and baboon models were highly similar to human but showed much less variability in energy minimized models. Our findings show that not all key sites in apo(a) are highly solvent exposed, but the flexibility of human apo(a) structure suggests the possibility of conformational changes that could alter their accessibility.