The objective of this study is to analyze the alterations in bone mineral density and bone and calcium-phosphorus metabolism in patients with calcium nephrolithiasis. We designed a study with 182 patients who were distributed among three groups: group O, 56 patients without nephrolithiasis; group A, 67 patients with calcium nephrolithiasis and mild lithogenic activity; and group B, 59 patients with calcium nephrolithiasis and severe lithogenic activity. Metabolic parameters of blood and urine that were related to calcium-phosphorous and bone metabolism and bone densitometry were assessed in all patients. A comparative study was performed on the variables of bone and calcium-phosphorus metabolism and bone densitometry as well as the presence or absence of osteopenia/osteoporosis. The patients in group B had a greater loss of bone mineral density, measured by the T-score, than the patients in groups O and A. Moreover, the proportion of patients in group B with osteopenia/osteoporosis was statistically significantly higher than the proportion of patients in groups O and A. We observed higher values of calciuria, fasting calcium/creatinine ratio, and 24-h calcium/creatinine among the patients in group B compared to the other two groups. Calciuria, citraturia, and fasting calcium/creatinine were independent factors that showed a relationship with severe lithogenic activity compared to the control group, and β-crosslaps is an independent factor that has a relationship with severe lithogenic activity as compared to mild lithogenic activity. Patients with calcium lithiasis and severe lithogenic activity have a greater loss in bone mineral density and therefore a greater risk of osteopenia/osteoporosis.