Until the advent of a vaccine, the most common cause of bacterial meningitis in Australia used to be Haemophilus influenzae type b (Hib). Since a vaccine was introduced, the two most common bacterial causes of meningitis in children are Neisseria meningitidis and Streptococcus pneumoniae. Viral meningitis is usually much less severe than bacterial meningitis, except in cases where the virus has caused encephalitis as well as meningitis. Viral causes of meningitis or encephalitis include varicella zoster, influenza, mumps, measles and until recently, polio. Many of these infections can be prevented with immunization, and following extensive preventive programmes for these viruses, enteroviruses have now become the most common cause of viral meningitis. Fungal infections of the central nervous system may also occur. The most common form of fungal meningitis is caused by the fungus Cryptococcus neoformans. Cryptococcal meningitis is common in AIDS patients. Although treatable, fungal meningitis often recurs in nearly half of affected persons. Arboviruses are the primary cause of acute encephalitis whilst herpes viruses are the other major cause of encephalitis in the developed world. Despite advances in antiviral therapy over the past two decades, herpes simplex encephalitis (HSE) remains a serious illness with significant risks of morbidity and death. The accurate diagnosis of encephalitis and meningitis due to infectious agents has been difficult using traditional methods. The introduction of molecular diagnostic assays has greatly facilitated their diagnosis, but clinical (CSF) samples need to be collected early in the infection process to maximize the likelihood of pathogen detection.