The goal for this study was to investigate if proton MRS (1H-MRS) and out-of-phase and in-phase MRI can quantify the fat deposition in bone marrow within the lumbar vertebra that can be used to distinguish well between osteoporosis patients and healthy control subjects. Sixty-eight subjects participated in this study. The diagnostic results from dual-energy x-ray absorptiometry served as the gold standard, which was able to separate the subjects into osteoporosis (38 subjects) and non-osteoporosis group (30 subjects). Then the 68 subjects were further scanned by 1H-MRS and in-phase and out-of-phase MRI and the findings from the imaging methods were also compared and analyzed. It was found that the measured signal intensity ratio (SIR), lipid-water ratio (LWR) and fat fraction (FF) in L2 vertebra from the two imaging methods were able to identify the fat deposition in bone marrow, which could be used to diagnose osteoporosis. Diagnostic accuracy for osteoporosis based on identified SIR, LRW and FF was analyzed by using ROC curves. Our findings suggested that statistically significant differences were identified between osteoporosis patients and healthy subjects. The sensitivity and specificity equal to 78.9 and 75.9 for SIR, 79.2 and 66.7 for LRW, 71.4 and 72.4 for FF, can be achieved when fat deposition-related parameters in bone marrow from the lumbar vertebra are used as classifiers. Our results showed that fat deposition-related parameters including fat content in bone marrow and water content in the lumbar vertebra are clearly different between the osteoporosis and non-osteoporosis group, suggesting that both 1H-MRS and in-phase and out-of-phase MRI can be used for diagnosing osteoporosis and monitoring its progression.