Thyroid hormones have a catabolic effect on bone homeostasis. Hence, this study aimed to evaluate serum vitamin D, calcium, and phosphate and bone marker levels and bone mineral density (BMD) among patients with different thyroid diseases. This cross-sectional study included patients with underlying thyroid diseases (n = 64, hyperthyroid; n = 53 euthyroid; n = 18, hypothyroid) and healthy controls (n = 64). BMD was assessed using z-score and left hip and lumbar bone density (g/cm²). The results showed that the mean serum vitamin D Levels of all groups was low (<50 nmol/L). Thyroid patients had higher serum vitamin D levels than healthy controls. All groups had normal serum calcium and phosphate levels. The carboxy terminal collagen crosslink and procollagen type I N-terminal propeptide levels were high in hyperthyroid patients and low in hypothyroid patients. The z-score for hip and spine did not significantly differ between thyroid patients and control groups. The hip bone density was remarkably low in the hyperthyroid group. In conclusion, this study showed no correlation between serum 25(OH)D levels and thyroid diseases. The bone markers showed a difference between thyroid groups with no significant difference in BMD.