The phenotypic diversity of familial hypercholesterolemia (FH) and lipoprotein(a) hyperlipidemia (Lp(a)-HLP), as defined risks for coronary artery disease with genetic background, and their frequent co-incidence with additional cardiovascular risk factors require a critical revisiting of the current diagnostic and screening criteria as well as therapeutic recommendations established for FH or isolated Lp(a)-HLP, since there is no clear guidance for patient stratification and disease management for combined cases. Further evaluation of the recent biomarkers and establishment of novel biomarkers are necessary for extended risk assessment of cardiovascular disease in FH or Lp(a)-HLP and to better understand the pathophysiology of these syndrome complexes. Lipoprotein apheresis is used as long-term treatment to reduce circulating lipoproteins in patients with severe FH and/or Lp(a)-HLP, particularly with multiple cardiovascular risks who are intolerant or insufficiently responsive to lipid-lowering drugs. Recent sophisticated analyses of molecular lipid species (lipidome) extended with transcriptomic and/or proteomic approaches may provide further lipid biomarkers for disease management of FH and/or Lp(a)-HLP, and relevant data for optimization of apheresis treatment. This review summarizes current studies investigating FH and Lp(a)-HLP as independent and combined cardiovascular risk factors, and some promising biomarker candidates for these entities.