Misfolding and subsequent self-assembly of protein molecules into various aggregates is a common molecular mechanism for a number of important human diseases. Curing protein misfolding pathologies and designing successful drugs for the inhibition or reversal of protein aggregation depends on understanding the peculiarities of the misfolding process. Protein aggregation is a very complex process characterized by a remarkable polymorphism, where soluble amyloid oligomers, amyloid fibrils and amorphous aggregates are found as final products. This polymorphism is associated with the existence of multiple independent and competing assembly pathways leading to aggregation. Regardless of the aggregation mechanism, soluble oligomers are inevitably formed during the self-association process. Some of these oligomers are now considered to be major initiators of the neurodegenerative cascades of corresponding diseases. However, not all oligomers are equally harmful, and several amyloidogenic proteins have been shown to form nontoxic oligomers, some of which were efficient fibrillation inhibitors. Unfortunately, the information on the structural properties of soluble oligomers and the mechanisms of their formation, interconversion and toxicity is sparse. This review provides an overview of some topics related to soluble oligomers and represents several illustrative examples of toxic, nontoxic, productive and off-pathway amyloid oligomers.