The diagnosis of bacterial overgrowth can be made by physicians in various ways.
Malabsorption can be detected by a test called the D-xylose test.
 Xylose is a sugar that does not require enzymes to be digested.
The D-xylose test involves having a patient drink a certain quantity of D-xylose, and measuring levels in the urine and blood; if there is no evidence of D-xylose in the urine and blood, it suggests that the small bowel is not absorbing properly (as opposed to problems with enzymes required for digestion).

The gold standard for detection of bacterial overgrowth is the aspiration of more than 10⁵ bacteria per millilitre from the small bowel.
The normal small bowel has less than 10⁴ bacteria per millilitre.
Some experts however, consider aspiration of more than 10³ positive if the flora is predominately colonic type bacteria as these types of bacteria are considered pathological in excessive numbers in the small intestine.
The reliability of aspiration in the diagnosis of SIBO has been questioned as SIBO can be patchy and the reproducibility can be as low as 38 percent.
Breath tests have their own reliability problems with a high rate of false positive.
Some doctors factor in a patients' response to treatment as part of the diagnosis.

Breath tests have been developed to test for bacterial overgrowth.
These tests are either based on bacterial metabolism of carbohydrates to hydrogen, methane, or hydrogen sulfide, or based on the detection of by-products of digestion of carbohydrates that are not usually metabolized.
The hydrogen breath test involves having the patient fast for a minimum of 12 hours then having them drink a substrate usually glucose or lactulose, then measuring expired hydrogen and methane concentrations typically over a period of several hours.
 It compares well to jejunal aspirates in making the diagnosis of bacterial overgrowth.
Carbon-13 (¹³C) and carbon-14 (¹⁴C) based tests have also been developed based on the bacterial metabolism of D-xylose.
 Increased bacterial concentrations are also involved in the deconjugation of bile acids.
 The glycocholic acid breath test involves the administration of the bile acid ¹⁴C glychocholic acid, and the detection of ¹⁴CO₂, which would be elevated in bacterial overgrowth.

Blood tests may check for the anti-CdtB and anti-vinculin biomarkers which are highly specific, but have low sensitivity, and may thus rule in, but not rule out, a diagnosis.

Some patients with symptoms of bacterial overgrowth will undergo upper endoscopy, or visualization of the stomach and duodenum with an endoscopic camera.
 Biopsies of the small bowel in bacterial overgrowth can mimic those of celiac disease, making the diagnosis more challenging.
 Findings include blunting of villi, hyperplasia of crypts and an increased number of lymphocytes in the lamina propria.

MR enterography may detect small bowel strictures without the use of radiation.
Capsule endoscopy may then be used to detect small bowel transit time if no strictures are found.
Antroduodenal manometry may also be used to evaluate motility.
However, it is a more difficult test for patients to endure and is not as widely available.

However, some physicians suggest that if the suspicion of bacterial overgrowth is high enough, the best diagnostic test is a trial of treatment.
 If the symptoms improve, an empiric diagnosis of bacterial overgrowth can be made.
The diagnosis of bacterial overgrowth can be made by physicians in various ways. Malabsorption can be detected by a test called the D-xylose test.  Xylose is a sugar that does not require enzymes to be digested. The D-xylose test involves having a patient drink a certain quantity of D-xylose, and measuring levels in the urine and blood; if there is no evidence of D-xylose in the urine and blood, it suggests that the small bowel is not absorbing properly (as opposed to problems with enzymes required for digestion).
The gold standard for detection of bacterial overgrowth is the aspiration of more than 10⁵ bacteria per millilitre from the small bowel. The normal small bowel has less than 10⁴ bacteria per millilitre. Some experts however, consider aspiration of more than 10³ positive if the flora is predominately colonic type bacteria as these types of bacteria are considered pathological in excessive numbers in the small intestine. The reliability of aspiration in the diagnosis of SIBO has been questioned as SIBO can be patchy and the reproducibility can be as low as 38 percent. Breath tests have their own reliability problems with a high rate of false positive. Some doctors factor in a patients' response to treatment as part of the diagnosis.
Breath tests have been developed to test for bacterial overgrowth. These tests are either based on bacterial metabolism of carbohydrates to hydrogen, methane, or hydrogen sulfide, or based on the detection of by-products of digestion of carbohydrates that are not usually metabolized. The hydrogen breath test involves having the patient fast for a minimum of 12 hours then having them drink a substrate usually glucose or lactulose, then measuring expired hydrogen and methane concentrations typically over a period of several hours.  It compares well to jejunal aspirates in making the diagnosis of bacterial overgrowth. Carbon-13 (¹³C) and carbon-14 (¹⁴C) based tests have also been developed based on the bacterial metabolism of D-xylose.  Increased bacterial concentrations are also involved in the deconjugation of bile acids.  The glycocholic acid breath test involves the administration of the bile acid ¹⁴C glychocholic acid, and the detection of ¹⁴CO₂, which would be elevated in bacterial overgrowth.
Blood tests may check for the anti-CdtB and anti-vinculin biomarkers which are highly specific, but have low sensitivity, and may thus rule in, but not rule out, a diagnosis.
Some patients with symptoms of bacterial overgrowth will undergo upper endoscopy, or visualization of the stomach and duodenum with an endoscopic camera.  Biopsies of the small bowel in bacterial overgrowth can mimic those of celiac disease, making the diagnosis more challenging.  Findings include blunting of villi, hyperplasia of crypts and an increased number of lymphocytes in the lamina propria.
MR enterography may detect small bowel strictures without the use of radiation. Capsule endoscopy may then be used to detect small bowel transit time if no strictures are found. Antroduodenal manometry may also be used to evaluate motility. However, it is a more difficult test for patients to endure and is not as widely available.
However, some physicians suggest that if the suspicion of bacterial overgrowth is high enough, the best diagnostic test is a trial of treatment.  If the symptoms improve, an empiric diagnosis of bacterial overgrowth can be made.
Small intestinal bacterial overgrowth