Acute and chronic diseases of the organs are treated in patients using a rational, multi-tier approach. A patient can be 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.