Atherosclerosis is a disease characterized by plaque formation due to an accumulation of fat, cholesterol, and immune cells in the walls of arteries. If a plaque ruptures, an occlusive thrombosis may form that causes either a heart attack or stroke. Macrophages express CB-2 receptors, and are one type of immune cell that plays a role in plaque destabilization and rupture. Endocannabinoids anandamide (AEA) and 2-arachidonyl glycerol (2-AG) have been found to have activity on CB-1 and CB-2 receptors throughout the body and immune system. In this study, we investigated several sample preparation options for the LC-MS quantification of AEA and 2-AG from plasma and aortic tissue. The extractions considered included liquid–liquid (LLE), solid-phase (SPE), and supported liquid (SLE). Some extraction protocols yielded high analyte recovery and prevention of 1-AG/2-AG isomerization. Our results indicate that a liquid-liquid extraction using toluene yields the highest recovery for both analytes, coupled with low ionization suppression in the mass spectrometer. This extraction and corresponding LC-MS/MS assay provides a simple, high throughput mechanism for the quantification of 2-AG and AEA in matrices relevant to the study of endocannabinoids’ role in atherosclerosis.