Methods of the invention involve determining a patient's compliance with a cholesterol lowering therapy. In certain aspects, the invention provides methods that involve conducting a first assay to determine a cholesterol biomarker level in a first sample from a patient prior to the patient undergoing a cholesterol lowering therapy. The methods may also involve conducting a second assay to determine a cholesterol level in a second sample obtained from the patient after the patient has started undergoing a cholesterol lowering therapy. Additionally, the methods involve associating the cholesterol level and the cholesterol biomarker level in which the association allows for the determination of the patient's compliance with the cholesterol lowering therapy.