Recent developments in the collection and analysis of cellular multilayered data in large cohorts with extensive organismal phenotyping promise to reveal links between genetic variation and biological processes. The use of these cellular resources as models for human biology — known as 'cellular phenotyping' — is likely to transform our understanding of the genetic and long-term environmental influences on complex traits. I discuss the advantages and caveats of a deeper analysis of cellular phenotypes in large cohorts and assess the methodological advances, resource needs and prospects of this new approach.