The growing prevalence of disorders of lipid and sterol homeostasis such as obesity and atherosclerosis in Western societies has increased demand for the development of therapies for their prevention and treatment. Crucial for this development is an understanding of the underlying cellular mechanisms which are involved in both healthy and diseased states. However, gaps remain in our knowledge of fundamental processes, such as intracellular sterol transport, lipid storage and mobilisation. Functional genomic strategies, such as genome-wide gene knockdown screens, are increasingly being exploited as powerful strategies to fill these gaps. This review discusses experimental approaches and findings in recent functional genomics studies of sterol and lipid biology, both in model organisms and human cells.