Objectives: Premature osteoporosis is one of the long term complications of Systemic Lupus Erythematosus (SLE). Recent studies showed that increased level of homocysteine was detected in SLE patients and it was associated with deterioration of bone health. The aim of this study was to determine the association between homocysteine and biochemical parameters of bone metabolism in SLE patients. Subjects and methods: Thirty-nine female patients who fulfilled American College of Rheumatology 1997 criteria for SLE under 50 years old and twelve healthy female as control group were studied. Various laboratory parameters including serum homocysteine, folic acid, vitamin B6, vitamin B12, bCTx, osteocalcin, MDA, and RANKL were measured. Results: This study found that significantly higher levels of homocysteine were found in SLE patients (p=0.010). There was also a significantly higher level of MDA and RANKL in SLE patient (p=0.042, p=0.030). Whereas, the folic acid, vitamin B6, vitamin B12, bCTX, and osteocalcin levels were not statistically different between SLE patients and control group. High homocysteine level was significantly associated with increased levels of bCTx (p=0.000, r=0.943), MDA (p=0.002, r=0.731), and RANKL (p=0.000, r=0.758). High level of homocysteine associated with decreased levels of osteocalcin (p=0.000, r=-0.771), folic acid (p=0.000, r=-0.734), vitamin B6 (p=0.046, r=-0.332). But an insignificant relationship was found between serum homocysteine and vitamin B12 (p=0.080, r=-0.284). Conclusion: Bone diminution in SLE seems to be attributable by homocysteine that influence bone formation and bone resorption process.