Multicellular systems develop from one cell to form complex structures through a series of spatio-temporally coordinated events. A key aspect of development is the acquisition of cell identity. During this process, cell-to-cell variability plays a major role to prime cell fate decision. External signals and transcriptional differences have been extensively used to explain cellular heterogeneity. Now, accumulating evidence demonstrates that intrinsic metabolic states contribute to cell fate decision as well. Among metabolites, lipids are abundant and have fundamental roles in several biological functions going from the regulation of gene expression and membrane trafficking, to being the main constituents of cell membranes. Moreover, a few studies uncovered an unexpected degree of cell-to-cell variability for some lipids, suggesting that lipid heterogeneity may contribute to the emergence of tissue patterning.