Many people find complex carbohydrates are problematic primarily due to the state of their digestive system. The GAPS diet is designed for to help people with intestinal permeability, which is often characterised by:

Dysbiosis: An imbalance of gut bacteria, where harmful bacteria may outnumber beneficial ones.
Inflammation: The intestinal tract is often inflamed and damaged, reducing its ability to function properly.
Impaired Enzyme Production: The gut may not produce enough digestive and brush border enzymes needed to break down complex carbohydrates effectively.

Here are points to explain why complex carbohydrates are restricted on the GAPS diet:

1. Difficulty in Digestion: Complex carbohydrates, such as those found in grains, starchy vegetables, and legumes, consist of long chains of sugar molecules (polysaccharides). For individuals with damaged gut lining and insufficient or imbalanced digestive enzymes, these complex structures are difficult to break down into simpler sugars.
2. Feeding Pathogenic Bacteria: When complex carbohydrates are not fully digested in the small intestine, they pass into the large intestine. Here, they can be fermented by opportunistic and pathogenic bacteria, leading to an overgrowth of these undesirable microorganisms. This fermentation process produces gas, bloating, discomfort, and can further contribute to dysbiosis and inflammation.
3. Increased Intestinal Permeability (“Leaky Gut”): The GAPS diet theory suggests that undigested food particles, including complex carbohydrates, can irritate the intestinal lining, potentially contributing to or worsening “leaky gut” (increased intestinal permeability). This allows toxins and undigested food components to enter the bloodstream, potentially triggering systemic inflammation and other health issues.
4. Specific Carbohydrate Diet (SCD) Basis: The GAPS diet is based on the Specific Carbohydrate Diet (SCD), which strictly eliminates all disaccharides and polysaccharides, but keeps monosaccharides. The rationale is that only monosaccharides (the simplest sugars) are easily absorbed without causing problems in a compromised gut.

By temporarily removing complex carbohydrates, the GAPS diet can:

Starve problematic bacteria: Without their preferred food source (undigested complex carbs), the growth of pathogenic bacteria is intended to be limited.
Allow the gut to heal: Reducing the digestive burden and irritation from complex carbohydrates is thought to give the intestinal lining a chance to repair itself.
Reduce symptoms: Many people with digestive issues experience relief from symptoms like bloating, gas, and pain when complex carbs are removed.

While complex carbohydrates are generally considered healthy and beneficial for most people due to their fibre content and slow release of energy, for those on the GAPS diet with significant gut dysfunction, they are seen as a hindrance to healing. In the reintroduction phase the GAPS diet gradually reintroduces foods when the gut health has improved sufficiently.