Currently, one of the fundamental problems in the study of membrane function and morphology is that the roles of proteins and lipids are usually investigated separately. In most cases proteins are predominant, with lipids taking a subsidiary role. This polarised view is in part due to the more straightforward and familiar techniques used to investigate proteins. Here, we summarise how phospholipids can be studied in cells with new tools that can acutely (rapidly and specifically) modify phospholipid composition of membranes in subcellular compartments. We point out some of the important physical effects that phosphoinositides in particular can have in altering membrane bilayer morphology, and provide specific examples to illustrate the roles that these phospholipids may play in maintaining the geometry of endomembranes.