One outstanding fundamental question in molecular biology asks how organismal, tissue and cellular complexity is achieved from a fixed number of genes that are present in all cells. Many factors that effect gene diversity have been identified including alternative splicing, of which intron retention (IR) is the least understood. IR has been widely regarded as a pathological failure in the splicing machinery’s excision of intronic sequences from pre-messenger RNAs, but a role in normal physiology has not previously been identified. Using mRNA-seq and a novel algorithm, IRFinder, we measured differential IR in FACS purified cells at three progressive stages of normal mature mouse granulopoiesis; promyelocytes, myelocytes and granulocytes. We found that IR affects at least 86 genes, including those specific to granulocytes (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the downregulation of the respective proteins measured by mass spectrometry and correlated with lower levels of splicing factors responsible for exon definition. The genes affected by IR were conserved between human and mouse. Chemical and siRNA inhibition of nonsense-mediated decay (NMD) in granulocytes resulted in marked accumulation of many intron retaining mRNAs, indicating that IR triggers NMD to downregulate mRNA and protein expression. Analysis of nascent RNA transcripts demonstrated that IR-mediated NMD occurred independently of transcriptional regulation in mRNA expression control. Enforced haemopoietic re-expression of ‘intronless’ Lmnb1 in vivo, which displayed high levels of IR across multiple introns, decreased granulocyte numbers in the peripheral blood, increased nuclear volume by 30% and altered nuclear morphology. Our data show that IR coupled with NMD is yet another mechanism by which gene expression is controlled during normal granulopoiesis1 and may be of broader significance in mammalian biology.