Homocystinuria and Marfan syndrome represent distinct genetic conditions that share phenotypically similar skeletal features. An overview of the current understanding of genetic and physiologic contributing to the etiology of these conditions is summarized. The focus of this review is to explore the present understanding of the pathophysiology of Marfan syndrome and homocystinuria relative to the occurrence of osteoporosis in both conditions. Osteoporosis has been reported in association with homocystinuria. However, evidence supporting an association of osteoporosis with Marfan syndrome is equivocal and sources of ambiguity are critically reviewed. Advisability and approaches to bone mineral density monitoring in patients with Marfan syndrome or homocystinuria to inform clinical management are discussed. Finally, future research foci are proposed which will improve understanding of association of osteoporosis with Marfan syndrome or homocystinuria.