Acute and chronic diseases of the organs are treated using a rational, multi-tier approach. A patient is pretreated with growth factor proteins or gene therapy, followed by the administration of adult stem cells or other cell therapy. The patient can be a fetus treated in utero or removed from the womb. The progress of treatment is monitored by ultrasound, MRI, CAT scan, cardiac echo, EEG, EKG, EMG or blood tests, with growth factor treatment and/or stem cell administration adjusted according to the results of the monitoring or clinical status of the patient. Organ disease is also treated by a method that comprises administration of a therapeutically effective amount of a growth factor protein by oral inhalation or intranasal therapy. Diseases affecting organs such as the brain, spinal cord, pancreas, liver, kidney, muscle, heart and upper and lower gastrointestinal tracts are treated using the present method. A device for treatment is disclosed. CPK is utilized to assess the treatment of muscle disease.