Habitat complexity is one of the most important factors structuring biotic assemblages, yet we still lack basic understanding of the underlying mechanisms. Although it is one of the primary targets in conservation management, no methods are available for comparing complexity across ecosystems, and system-specific qualitative assessment predominates. Despite its overwhelming importance for faunal diversity and abundance, there has been surprisingly little interest in examining its effects on other community and ecosystem attributes. We discuss possibilities of such effects, outlining potentially fruitful areas for future research, and argue that complexity may be implicated in community persistence and ecosystem stability by acting as a decoupling mechanism in predator-prey interactions. We provide a brief overview of methods used to quantify complexity in different ecosystems, highlighting contributions of the current issue of Hydrobiologia, and discuss potential application of these approaches for cross-ecosystem comparisons. Better understanding of the role of habitat complexity resulting from such comparisons is critically important for preservation of biodiversity and ecosystem function in an era of unprecedented habitat loss.