A Gram stain is used, along with a culture of the material from an infected site, to identify the cause of a bacterial infection. The Gram stain provides preliminary results on whether bacteria are present and the general type, such as the shape and whether they are Gram-positive or Gram-negative.

Often, detecting the presence of bacteria and determining whether an infection is caused by a microbe that is Gram-positive or Gram-negative will be sufficient to allow a healthcare practitioner to prescribe treatment with an appropriate antibiotic while waiting for more specific tests, such as a culture, to be completed. Absence or presence of white blood cells in the Gram stain can help establish that an adequate sample was obtained as white blood cells are frequently present with an infection.

A Gram stain may also be performed as part of the evaluation of a culture. When bacteria grow on/in a nutrient media in the laboratory, a Gram stain is performed to help determine the type of bacteria present and to help determine what other tests may need to be performed to definitively identify the cause of infection.

Fungi, including yeast, may also be detected with a Gram stain.

A Gram stain is typically ordered along with a culture when a bacterial or sometimes fungal infection is suspected. It is also usually performed when the result of a culture is positive, on a sample of the bacteria grown in the culture. Test results are reported promptly to help guide treatment.

A negative Gram stain is often reported as "no organism seen." This may mean that there is no bacterial infection present or that there were not enough bacteria present in the sample to be seen with the stain under a microscope.

Positive Gram stain results usually include a description of what was seen on the slide. This typically includes:

• Whether the bacteria are Gram-positive (purple) or Gram-negative (pink) 
• Shape — round (cocci) or rods (bacilli)
• Size, relative quantity, and/or arrangement of the bacteria, if relevant
• Whether there are bacteria present within other cells (intracellular) 
• Presence of red blood cells or white blood cells
• Fungi (in the form of yeasts or molds) may be seen on a Gram stain and are reported. Yeast may appear as single cells that may have buds, while molds may appear as a wide variety of plant-like branches called hyphae. Further testing may be performed to identify the specific type. (See Fungal Tests for more on this.)

This information, along with signs and symptoms and other clinical findings, will help the healthcare practitioner decide which treatment may be most effective, sometimes before culture results are available.

However, Gram stain results are usually considered preliminary, and results of a culture and/or other tests such as antigen and antibody testing for particular types of bacteria are necessary to confirm a diagnosis. Sometimes, susceptibility testing is necessary to determine which antibiotic will be most effective in treating the infection.

A few examples of some medically significant bacteria and what they look like on a Gram stain include:

• Gram-positive cocci—Staphylcoccus aureus (Staph aureus) can cause skin infections and toxic shock syndrome; Streptococcus pneumoniae can cause pneumonia.
• Gram-negative cocci—Neisseria meningitidis causes meningitis while Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea.
• Gram-positive bacilli—Bacillus anthracis (anthrax) can cause skin infections or pneumonia (also a bioterrorism agent); Listeria monocytogenes can cause foodborne illnesses.
• Gram-negative bacilli—Escherichia coli is a common cause of urinary tract infections.

Samples such as blood and cerebrospinal fluid are generally sterile. Bacteria are not usually present in these samples when there is no bacterial infection. Bacteria may initially be present in low numbers with an infection, and this type of sample may require extra processing in order to concentrate the bacteria so that they can be detected by a Gram stain.

Other body fluids and sites, such as sputum or skin, typically have cells and normal flora present in addition to any bacteria that are causing an infection. Gram stains on these types of samples require careful examination by a trained laboratorian to determine which cells may be normal and which may be due to an infection.

Bacterial infections should not be ignored, even if the symptoms are mild. Prompt treatment can limit their spread and severity. If left untreated, bacterial infections can spread and may eventually cause tissue and organ damage.

Viruses cannot be detected with a Gram stain.

If a healthcare practitioner suspects that a person has a mycobacterial infection, such as tuberculosis, an AFB (acid-fast bacillus) smear and culture may be ordered on a sputum sample instead of a Gram stain and culture.