Background In SLE, both disease-specific and traditional risk factors are important. Increased serum homocysteine levels are seen in approximately 15% of patients with systemic lupus erythematosus and are associated with an increased risk of atherothrombotic events in this population. The serum level of homocysteine in patients with lupus nephritis has not been well described. Methods We performed a retrospective review of patients who had both biopsy-proven lupus nephritis (class II-VI) and measured homocysteine levels during routine evaluation. Clinical and laboratory data were obtained from reviews of medical records. Results Of the 15 patients with lupus nephritis, 10 had elevated homocysteine levels. The ages ranged from 21-68 years and were predominately African-American females. There were three patients with class III, one with class III-V, two with class IV, and two with class V lupus nephritis. Two patients had more than one biopsy each, one with class III, IV-V, and one with III and IV. At the time, when the serum homocysteine level was measured, of the 10 patients with elevated homocysteine levels, five patients had positive anti-dsDNA, and four had hypocomplementemia predominately low C3 (three patients). All patients were on hydroxychloroquine. Conclusions This study demonstrates that patients with lupus nephritis are at a higher risk (66.6%) for developing elevated homocysteine levels.