The purpose of a CSF analysis is to diagnose medical disorders that affect the central nervous system. Some of these conditions include:

• viral and bacterial infections, such as meningitis, West Nile virus, herpesvirus, and encephalitis
• tumors or cancers of the nervous system
• syphilis, a sexually transmitted disease
• bleeding (hemorrhaging) around the brain and spinal cord
• multiple sclerosis, a disease that affects the myelin coating of the nerve fibers of the brain and spinal cord
• Guillain-Barré syndrome, an inflammation of the nerves.
• Early-onset Alzheimer's disease. The levels of two substances known as amyloid beta(1-42) and phosphorylated tau in CSF appear to be useful diagnostic markers for early-onset Alzheimer's.

CSF analysis is also used in forensic investigations to identify the presence of illicit drugs (e. g., heroin) or poisons in the bodies of murder, accidental overdose, or suicide victims.

In some circumstances, a lumbar puncture to withdraw a small amount of CSF for analysis may lead to serious complications. Lumbar puncture should be performed only with extreme caution, and only if the benefits are thought to outweigh the risks, in certain conditions. For example, in people who have blood clotting (coagulation) or bleeding disorders, lumbar puncture can cause bleeding that can compress the spinal cord. If there is a large brain tumor or other mass, removal of CSF can cause the brain to droop down within the skull cavity (herniate), compressing the brain stem and other vital structures, and leading to irreversible brain damage or death. These problems are easily avoided by checking blood coagulation through a blood test and by doing a computed tomography scan (CT) or magnetic resonance imaging (MRI) scan before attempting the lumbar puncture. In addition, a lumbar puncture procedure should never be performed at the site of a localized skin infection on the lower back because the infection may be introduced into the CSF and may spread to the brain or spinal cord.

The procedure to remove cerebrospinal fluid is called a lumbar puncture, or spinal tap, because the area of the spinal column used to obtain the sample is in the lumbar spine, or lower section of the back. In rare instances, such as a spinal fluid blockage in the middle of the back, a doctor may perform a spinal tap in the neck. The lower lumbar spine (usually between the vertebrae known as L4–5) is preferable because the spinal cord stops near L2, and a needle introduced below this level will miss the spinal cord and encounter only nerve roots, which are easily pushed aside.

A lumbar puncture takes about 30 minutes. Patients can undergo the test in a doctor's office, laboratory, or outpatient hospital setting. Sometimes it requires an inpatient hospital stay. If the patient has spinal arthritis, is extremely uncooperative, or obese, it may be necessary to introduce the spinal needle using x-ray guidance.

In order to get an accurate sample of cerebrospinal fluid, it is critical that a patient is in the proper position. The spine must be curved to allow as much space as possible between the lower vertebrae, or bones of the back, for the doctor to insert a lumbar puncture needle between the vertebrae and withdraw a small amount of fluid. The most common position is for the patient to lie on his or her side with the back at the edge of the exam table, head and chin bent down, knees drawn up to the chest, and arms clasped around the knees. (Small infants and people who are obese may need to curve their spines in a sitting position.) People should talk to their doctor if they have any questions about their position because it is important to be comfortable and to remain still during the entire procedure. In fact, the doctor will explain the procedure to the patient (or guardian) so that the patient can agree in writing to have it done (informed consent). If the patient is anxious or uncooperative, a short-acting sedative may be given.

During a lumbar puncture, the doctor drapes the back with a sterile covering that has an opening over the puncture site and cleans the skin surface with an antiseptic solution. Patients receive a local anesthetic to minimize any pain in the lower back.

The doctor inserts a hollow, thin needle in the space between two vertebrae of the lower back and slowly advances it toward the spine. A steady flow of clear cerebrospinal fluid, normally the color of water, will begin to fill the needle as soon as it enters the spinal canal. The doctor measures the cerebrospinal fluid pressure with a special instrument called a manometer and withdraws several vials of fluid for laboratory analysis. The amount of fluid collected depends on the type and number of tests needed to diagnose a particular medical disorder.

In some cases, the doctor must remove and reposition the needle. This occurs when there is not an even flow of fluid, the needle hits bone or a blood vessel, or the patient reports sharp, unusual pain.

Patients can go about their normal activities before a lumbar puncture. Experts recommend that patients relax before the procedure to release any muscle tension, since the lumbar puncture needle must pass through muscle tissue before it reaches the spinal canal. A patient's level of relaxation before and during the procedure plays a critical role in the test's success.

After the procedure, the doctor covers the site of the puncture with a sterile bandage. Patients must avoid sitting or standing and remain lying down for as long as six hours after the lumbar puncture. They should also drink plenty of fluid to help prevent lumbar puncture headache, which is discussed in the next section.

For most people, the most common side effect after the removal of CSF is a headache. This occurs in 10–30% of adult patients and in up to 40% of children. It is caused by a decreased CSF pressure related to a small leak of CSF through the puncture site. These headaches usually are a dull pain, although some people report a throbbing sensation. A stiff neck and nausea may accompany the headache. Lumbar puncture headaches typically begin within two days after the procedure and persist from a few days to several weeks or months.

Since an upright position worsens the pain, patients with a lumbar puncture headache can control the pain by lying in a flat position and taking a prescription or non-prescription pain relief medication, preferably one containing caffeine. In rare cases, the puncture site leak is "patched" using the patient's own blood.

People should talk to their doctor about complications from a lumbar puncture. In most cases, this test to analyze CSF is a safe and effective procedure. Some patients experience pain, difficulty urinating, infection, or leakage of cerebrospinal fluid from the puncture site after the procedure.

Normal CSF is clear and colorless. It may be cloudy in infections; straw- or yellow-colored if there is excess protein, as may occur with cancer or inflammation; blood-tinged if there was recent bleeding; or yellow to brown (xanthochromic) if caused by an older instance of bleeding.

A series of laboratory tests analyze the CSF for a variety of substances to rule out possible medical disorders of the central nervous system. The following are normal values for commonly tested substances:

• CSF pressure: 50–180 mmH2O
• glucose: 40%ndash;85 mg/dL
• protein: 15–50 mg/dL
• leukocytes (white blood cells) total less than 5 per mL
• lymphocytes: 60–70%
• monocytes: 30–50%
• neutrophils: none

Normally, there are no red blood cells in the CSF unless the needle passes though a blood vessel on route to the CSF. If this is the case, there should be more red blood cells in the first tube collected than in the last.

Abnormal test result values in the pressure or any of the substances found in the cerebrospinal fluid may suggest a number of medical problems including a tumor or spinal cord obstruction; hemorrhaging or bleeding in the central nervous system; infection from bacterial, viral, or fungal microorganisms; or an inflammation of the nerves. It is important for patients to review the results of a cerebrospinal fluid analysis with their doctor and to discuss any treatment plans.