Bone weakening can be affected by agents other than bone mineral density (BMD). Increased bone marrow fat may have a direct link to bone loss. This pilot study analyzes the relationship between bone marrow fat and BMD in subjects with normal and structurally weakened vertebrae. Twenty-six subjects underwent both dual-energy X-ray absorptiometry and proton MR spectroscopy of 71 lumbar vertebrae. Fifteen subjects had normal-appearing vertebrae on MRI, and 11 had signs of bone weakening. We found that high bone marrow fat did not consistently equate with low BMD. Bone marrow fat can indicate bone weakening nearly as well as BMD, but neither parameter alone is suitable to be used independently as an indicator. The bone marrow fat/BMD ratio showed significant diagnostic power to detect bone weakening, even in this relatively small subject sample. An inverse relationship between bone marrow fat and BMD could not be confirmed. Bone marrow fat can be used to diagnose reduced bone strength nearly as well as BMD. The bone marrow fat/BMD ratio is a significant diagnostic indicator of bone weakening.