The type I interferon response is a key part of the innate immune system, responding to infection and inducing an antiviral intracellular state. While there is known to be variability in this signalling pathway between individuals, alongside cell-to-cell heterogeneity in a genetically identical cell population, the basis of this variation is not fully understood. In this PhD, I established large-scale single-cell RNA sequencing experiments to study cellular variation in the innate immune response in fibroblasts of 70 healthy human individuals from the HipSci initiative. Chapter 2 describes optimisation of stimulation conditions to induce an antiviral response, and the experimental work carried out on the panel of donors. In Chapter 3, I analyse heterogeneity in resting (unstimulated) fibroblasts. By comparing to ex vivo skin data containing multiple cell types, I confirm the relative homogeneity of the in vitro cultured fibroblasts used, mapping to one sub-population of ex vivo skin fibroblasts. Using matched whole exome sequencing data, somatic mutations in sub-populations of cells within each donor were detected, and clonal populations identified. A novel computational method, cardelino, was developed for inference of the clonal tree configuration and the clone of origin of individual cells that have been assayed using scRNA-seq. Applying cardelino to 32 fibroblast lines identifies hundreds of differentially expressed genes between cells from different somatic clones, with cell cycle and proliferation pathways frequently enriched. Returning to innate immunity, Chapters 4 and 5 centre on variability in the type I interferon response. I first describe work linking variability in the innate immune response and evolutionary divergence across mammalian species. Focusing on human variability, the large dataset described above is used to characterise the innate immune response at single cell resolution, elucidating the dynamics of the response across donors in Chapter 4. Chapter 5 describes the application of quantitative trait loci approaches to innate immune phenotypes. This work characterises both inter- and intra-individual heterogeneity in innate immunity.