Human immunodeficiency virus (HIV) affects all organ systems. Infection of the heart can manifest with evidence of myocarditis, pericarditis, or cardiomyopathy. The most common gastrointestinal symptom is diarrhea, which can result from infection with a variety of bacterial, fungal, or protozoal organisms. In about 15% of cases, no pathogen is recognized and the diarrhea syndrome is termed AIDS enteropathy. Any portion of the alimentary tract can be affected as well as the liver, gallbladder, and pancreas. Cryptosporidium, a previously infrequent cause of human illness, has emerged as an important pathogen in the HIV-infected patient and is responsible for chronic diarrhea, cholecystitis, and biliary tract obstruction. Evidence of neurologic involvement is present in more than 80% of patients at the time of autopsy. Cryptococcal meningitis, toxoplasma encephalitis, and neurosyphilis are the most often encountered central nervous system infections. While all three are responsive to therapy, treatment must be prolonged or persist for the duration of the patient's life to avoid recurrence. Peripheral nervous system manifestations include myelopathy, myopathy, and a variety of peripheral neuropathies. Retinal infection with cytomegalovirus (CMV) and toxoplasma can lead to irreversible loss of vision. Cotton wool spots are a common benign physical finding that must be differentiated from the early signs of CMV or toxoplasma infection. Management of the HIV-infected patient, while most often conducted by specialists in Internal Medicine or Infectious Diseases, is often an issue for the emergency physician. Many of the commonly afforded therapies are reviewed. Part 1 of this two-part series discussed the pathophysiology and clinical expression, epidemiology, laboratory testing, and the general clinical manifestations of AIDS, as well as dermatologic, pulmonary, and cardiac symptoms. Part 2 discusses the gastrointestinal, neurologic, and ocular symptoms, as well as the treatment and management of the AIDS patient.