Methods and compositions are provided which contains preparations of calcium chelators, bisphosphonates, antibiotics, antimicrobial agents, cytostatic agents, calcium ATPase and pyrophosphatase pump inhibitors, calcium phosphate-crystal dissolving agents, agents effective against calcium phosphate-crystal nucleation and crystal growth, and/or a combination of supportive agents and which may be used for treating and or reducing pathological calcifications, the growth of Nanobacterium and calcification-induced diseases including, but not limited to, Arteriosclerosis, Atherosclerosis, Coronary Heart Disease, Chronic Heart Failure, Valve Calcifications, Arterial Aneurysms, Calcific Aortic Stenosis, Transient Cerebral Ischemia, Stroke, Peripheral Vascular Disease, Vascular Thrombosis, Dental Plaque, Gum Disease (dental pulp stones), Salivary Gland Stones, Chronic Infection Syndromes such as Chronic Fatigue Syndrome, Kidney and Bladder Stones, Gall Stones, Pancreas and Bowel Diseases (such as Pancreatic Duct Stones, Crohn's Disease, Colitis Ulcerosa), Liver Diseases (such as Liver Cirrhosis, Liver Cysts), Testicular Microliths, Chronic Calculous Prostatitis, Prostate Calcification, Calcification in Hemodialysis Patients, Malacoplakia, Autoimmune Diseases. Erythematosus, Scleroderma, Dermatomyositis, Antiphospholipid Syndrome, Arteritis Nodosa, Thrombocytopenia, Hemolytic Anemia, Myelitis, Livedo Reticularis, Chorea, Migraine, Juvenile Dermatomyositis, Grave's Disease, Hypothyreoidism, Type 1 Diabetes Mellitus, Addison's Disease, Hypopituitarism, Placental and Fetal Disorders, Polycystic Kidney Disease, Glomerulopathies, Eye Diseases (such as Corneal Calcifications, Cataracts, Macular Degeneration and Retinal Vasculature-derived Processes and other Retinal Degenerations, Retinal Nerve Degeneration, Retinitis, and Iritis), Ear Diseases (such as Otosclerosis, Degeneration of Otoliths and Symptoms from the Vestibular Organ and Inner Ear (Vertigo and Tinnitus)), Thyroglossal Cysts, Thyroid Cysts, Ovarian Cysts, Cancer (such as Meningiomas, Breast Cancer, Prostate Cancer, Thyroid Cancer, Serous Ovarian Adenocarcinoma), Skin Diseases (such as Calcinosis Cutis, Calciphylaxis, Psoriasis, Eczema, Lichen Ruber Planus), Rheumatoid Arthritis, Calcific Tenditis, Osteoarthritis, Fibromyalgia, Bone Spurs, Diffuse Interstitial Skeletal Hyperostosis, Intracranial Calcifications (such as Degenerative Disease Processes and Dementia), Erythrocyte-Related Diseases involving Anemia, Intraerythrocytic Nanobacterial Infection and Splenic Calcifications, Chronic Obstructive Pulmonary Disease, Broncholiths, Bronchial Stones, Neuropathy, Calcification and Encrustations of Implants, Mixed Calcified Biofilms, and Myelodegenerative Disorders (such as Multiple Sclerosis, Lou Gehrig's and Alzheimer's Disease) in humans and animals. The method comprises administering the various classes of compositions of the present invention, which together effectively inhibit or treat the development of calcifications in vivo.