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Even though the concept of modular organisation (modularity) was proposed a long time ago, a lot of unresolved questions remain. This concept is still not generally accepted or widely used. The term “modular organisation” is applied to various phenomena, from individual organisation to genome (genetic program) organisation and functioning. We discuss the problems of using the concept of modular organisation in the context of individual organisation using invertebrates as an example. The notions of “colonial” and “modular” organisms are still frequently used as synonyms. At the same time there are clear (precise) criteria for distinguishing between colonies of individuals and ‘super-individuals’ with modular organisation. One is physical continuity between organism parts either via permanent cytoplasm bridges between cells, or via specialised intercellular contacts integrating cells into tissues. One of the most problematic points is the definition of modules, the structural units (blocks) of modular organisms. The problem is the existence of different levels and different approaches to defining a ‘module’: morphological, structural, physiological, morphogenetic, etc. We propose that the most attractive and useful approach is the morphogenetic one: a ‘module’ is the result of a certain developmental process, i.e. morphogenetic programme. In most cases a modular individual is constructed with a different number of modules. However, the morphogenetic approach does not always make it easy to compare the organisation of even closely related species, as different ‘primary’ modules can merge into ‘secondary’ modules. Modular polymorphism raises more questions about how to define modules.