Test Overview of Comprehensive Stool Analysis Panel

The Stool Analysis Panel detects both beneficial and pathogenic microflora in the GI tract, including yeasts, bacteria, and parasites. It also provides a number of other markers of gut health.

Test Indications of Comprehensive Stool Analysis Panel

  • First-line test for evaluating Autism Spectrum Disorder (ASD), Pervasive Developmental Disorder (PDD), Asperger's Syndrome, Attention-Deficit Hyperactivity Disorder (ADD, ADHD), and learning disability.
  • First-line test for evaluating depression, anxiety, and other mood disorders.
  • First-line test for evaluating Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IBD), Crohn's Disease, and other intestinal complaints.
  • First-line test for evaluating autoimmune disorders, joint pain, and psoriasis.
  • First-line test for evaluating Chronic Fatigue Syndrome and Fibromyalgia.
  • Environmental toxicity.
  • Seizure disorders.

Sample Collection for Comprehensive Stool Analysis Panel

  1. Your doctor will provide you with the sample collection kit.
  2. The sample must be sent via overnight FedEx directly to the lab on a Monday through Thursday using the prepaid mailer provided.
  3. Detailed instructions are in the sample collection kit.

Your doctor or lab may have different instructions that supersede the above.

ICD-9 CODES for Comprehensive Stool Analysis Panel

112.9Yeast infection 
277.9Metabolic disorder 
279.9Immune system disorder 

CPT CODES for Comprehensive Stool Analysis Panel

82272Occult blood 
82492Quantitative chromatography 
82656Pancreatic elastase 
83986Stool pH 
87045Salmonella/Shigella bacterial culture 
87046Other aerobic bacterial culture 
87102Fungal culture 
87177*2Ova and parasitesTwo samples
87209*2Special smear for ova and parasitesTwo samples
87328Cryptosporidium immunoassay 
87329Heliobacter pylori immunoassay 
89125Fat stain 
89160Meat fiber 

Labs Performing Comprehensive Stool Analysis Panel Test

Name of LabLab CodeEstimated CostProcessing TimeComments
Great Plains  $3302-3 weeksCash discount and some insurance

Costs cited are subject to change and may be reduced by insurance or cash discounts and increased by sample collection fees.

Theory of Comprehensive Stool Analysis Panel

Digestion and Absorption

Stool Fats

  • Long-chain fatty acids are an indication of fat-malabsorption or maldigestion.
  • Short-chain fatty acids are necessary nutrients for colonocytes.

Meat Fibers

  • Undigested meat fibers in the stool are suggestive of poor digestion due to inadequate stomach acid.

Vegetable Fibers

  • Undigested vegetable fibers in the stool are suggestive of poor digestion.

Pancreatic Elastase

  • Low levels may indicate pancreatic insufficiency.


  • Presence may indicate poor absorption.

Bacterial Culture and Sensitivity

Beneficial Bacteria

  • We want to see high levels of these in the stool.
  • Help to prevent overgrowth of pathogenic bacteria.
  • Bifidobaster
  • Lactobacillus
  • E. coli

Pathogenic Bacteria

  • Salmonella
  • Shigella
  • Citrobacter
  • Klebsiella pneumoniae - associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS).
  • Staph aureus

Yeast Culture and Sensitivity

Fungal Culture

Fungal Sensitivity

  • Suggests which anti-fungal agents are useful in treating the yeast and fungi isolated.

Parasite Testing

  • Searches for evidence of parasites or their eggs (ova).
  • Due to the periodic life cycle of parasites, multiple specimens are examined.

Inflammatory Markers


  • Elevated levels are associated with inflammatory bowel disease and dysbiosis.


  • Elevated levels are associated with inflammatory bowel disease and dysbiosis.

White Blood Cells (WBC)

  • Elevated levels are associated with inflammatory bowel disease and dysbiosis.


  • Elevated levels are associated with inflammatory bowel disease and dysbiosis.

Stool Metabolic Markers

Stool pH

ELISA Immunoassays

Immunoassay reveals evidence of pathogen even when not culturable.

Helicobacter pylori



Giardia lamblia

Other Tests

Occult Blood

  • Detects hidden bleeding in the GI tract.
  • GI bleeding is considered to be due to cancer until proven otherwise.

Secretory Immunoglobulin A (SigA)

  • Generally beneficial - non-inflammatory defense against pathogens.
  • May be elevated or depleted in the presence of pathogens or food allergies.

References regarding Comprehensive Stool Analysis Panel

[GP] Great Plains Laboratory Physician Training lecture notes and documentation.

Unless specifically noted above, references used in the construction of this web page include the following:

[FDM] Lecture notes from Functional Medicine University.

[SCNM] Lecture notes from Southwest College of Naturopathic Medicine.

[UT] Lecture notes from the University of Tennessee graduate programs in Chemistry, Microbiology, and Biochemistry.