Deciphering the contribution of individual genes and in turn pathways to cellular processes can be complicated and is often based on prior knowledge or assumptions of gene function. Phenotype-driven mutagenesis screens based around n-ethyl-n-nitrosurea (ENU) have been successful in a wide range of physiological systems in identifying novel genes that contribute to a given phenotype. Here, we describe methodologies we have employed in analysing cellular phenotypes in pipelines of mutagenised mice. Examples of primary screens to identify outliers, and secondary screens to provide a more detailed characterisation are outlined.