The doctor diagnoses encephalitis or meningitis after a completing a thorough history (asking the patient questions) and examination. The examination includes special maneuvers to detect signs of inflammation of the membranes that surround the brain and spinal cord (meninges). Based on the history and examination, the doctor suggests specific tests to further help in determining the diagnosis.

Tests that are used in the evaluation of individuals suspected of having encephalitis or meningitis include evaluation of the blood for signs of infection and possible presence of bacteria, brain scanning (such as CT scanning or MRI scan), and cerebrospinal fluid analysis.

A lumbar puncture is the most common method of obtaining a sample of the fluid in the spinal canal (the cerebrospinal fluid or CSF) for examination. A lumbar puncture (an LP) is the insertion of a needle into the fluid within the spinal canal. It is termed a "lumbar puncture" because the needle goes into the lumbar portion of the back (the lower portion of the back). The needle passes between the bony parts of the spine until it reaches the cerebral spinal fluid. A small amount of fluid is then collected and sent to the laboratory for examination. The evaluation of the spinal fluid is usually necessary for the definite diagnosis and to help make optimal treatment decisions (such as the appropriate choice of antibiotics).

The diagnosis is confirmed by abnormal spinal fluid results and, in the case of an infection, by identifying the organism causing the infection. In patients with meningitis, the CSF fluid often has a low glucose (sugar) level and increased white blood cell count. In addition, the fluid can be used to identify some viral causes of meningitis (PCR or polymerase chain reaction) or be used to culture bacterial organisms causing the meningitis.

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