Sample preparation is the gateway to metabolomic analysis, the importance of which cannot be overemphasized. There are general rules of thumb for sample preparation that help maximize sample integrity and metabolite recovery. The wide range of variations in metabolite functional groups, polarity, sizes, and stability precludes the use of a single extraction method in metabolomic studies. Common extraction methods for polar metabolites that utilize trichloroacetic acid or aqueous acetonitrile are suitable for both nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis while others that use chloroform/methanol/water partition or boiling water may not. Control of extract pH is crucial for consistent NMR assignments and chemical derivatization-linked MS analysis. Sequential polar and lipid extractions reduce sample size requirement and provide a better coverage for direct-infusion MS analysis of lipids, possibly by removing interfering salts. Cleanup of sample extracts, such as removal of fine particles or interfering cations, is often necessary but should be limited to reduce loss of metabolites.