The rising incidence of cardiovascular and metabolic diseases in industrialized countries has led the pharmaceutical industry to make them key areas of drug development. These diseases imply a clustering of metabolic factors where lipid metabolites play a relevant role. Measurement of pharmacodynamic endpoints of drugs on lipid metabolism pathways and downstream biological processes appear crucial for a rational drug discovery/development. Fortunately, recent mass spectrometers with an enhanced sensitivity and resolution in combination with multivariate statistical analysis provide the practical possibility to analyze and measure wide portions of the lipidome. The final goal is to identify lipid signatures which fit with specific pharmacologic responses to therapeutic intervention. Focusing on applications of lipidomics for drug development this review outlines the methodological steps, from analytical measurements to data processing and to graphical representation, for an efficient implementation of informative lipid signatures.