Nature has created an immense combinatorial and structural heterogeneity among lipids. It is becoming increasingly accepted that the vast range of unique chemical entities encodes for distinct functions within biological systems. A unique group of lipids which stands out in terms of diversity as well as biological activity are inositol-containing lipids. The most well characterized inositol lipids are the phosphoinositides, phosphorylated derivatives of glycerophosphoinositol, which play a wide variety of cellular roles in many eukaryotic cells. Less well understood are ceramides containing inositol in fungi, and inositol glycolipids in pathogens. Here we review biochemical aspects of inositol-containing lipids with a focus on novel analytical procedures for their characterization.