Calcific tendinopathy of the tendons of the rotator cuff is common in adults. These calcifications tend to be reabsorbed after a period of acute pain. This study evaluated the morphologic characteristics of calcific deposits and the participation of phytate and osteopontin (OPN) in their development. Calcific deposits were removed from 21 patients with calcific tendinopathy by ultrasound-guided needle puncture under local anesthesia. The removed deposits were evaluated by scanning electron microscopy, X-ray diffraction and Fourier transform infrared spectroscopy. The amounts of calcium and phosphorus in the deposits were semi-quantitatively determined by energy dispersive X-ray analysis. Phytate was determined in 2 h urine samples, and OPN was extracted from a pool of deposits. The calcific deposits consisted of amorphous and poorly crystalline carbonated hydroxyapatite containing molecular water and organic matter. OPN was associated with the hydroxyapatite deposits. Phytate concentrations were significantly lower in the urine of patients with calcific tendinopathy than in healthy controls. The deficit in crystallization inhibitors such as phytate, and the presence of regulators such as OPN, may play important roles in the development of calcific tendinopathy.