Osteoporosis, a condition where the density of bone-mass decreases leading to fragile, weakened bones, has been strongly linked to homocystinuria (elevated urinary homocysteine) and associated with high homocysteine levels. Postmenopausal women are particularly at risk from low oestrogen levels. This in turn appears to raise homocysteine and increase the chance of developing osteoporosis later on in life.

A Japanese study followed 628 patients aged 65 years or older for one year after suffering a stroke. A dramatic increase in the number of subsequent hip fractures was evident, twice to four times higher than that expected in age-matched healthy control patients. Patients with homocystinuria also had an increased prevalence of skeletal abnormalities, including osteoporosis, which is a primary risk factor for hip fracture. Elevated homocysteine concentrations appears to be independently associated with both osteoporosis and the increased risk of hip fracture.