Abstract
BACKGROUND: Several molecular classification systems for bladder cancer have been proposed, but due to differences on how to define molecular subtypes, controversies and misunderstandings have arisen. OBJECTIVE: To discuss different aspects of the molecular classification of bladder cancer and to point to the consequences of using different conceptual approaches. To question some underlying assumptions when defining molecular subtypes. METHODS: To critically reflect on some of the principles and methods used when defining molecular subtypes. RESULTS: Depending on underlying assumptions and aims for the definitions of subtypes, different types of molecular subtypes will be arrived at. CONCLUSION: The underlying assumptions and their consequences must be better clarified when defining molecular subtypes.