The immune system is involved in modelling of tissue structures. Constant immune stimulation by microbiota can impact on colon development, immunity, and health of individuals. Highly dynamic stromal structure remodeling is demonstrated by 2-photon microscopy second-harmonic generation (SHG) imaging in the mucosa of mice transferred from germ-free (GF) to conventional (CV) conditions (microbiota colonization). In rat model, healthy colon mucosa of CV rats expresses more pro-inflammatory cytokines (IFNγ, IL1, TNFα) and TGFβ than GF rat mucosa. This more active network can also justify differences in stromal structures revealed by SHG. Analysis of SHG images proved significant differences in GF vs CV collagen architecture, suggesting direct effects of immunological network on it. Similarly, structural changes are well documented in both induced chronic colitis and carcinogenesis models. They show very similar trend in tissue fibrosis that starts early. Early peaks of INFγ and TGFβ1 expression were noted in both models. Azoxymethane carcinogenesis determined early increase of IL-6 and TGFβ1. This results suggest possible conditions for Th17 cell maturation with fostering carcinogenesis. Our results indicate a role of local pro-inflammatory/regulatory cytokines in remodelling the collagen scaffold under chronic inflammatory conditions. Stromal changes appears a suitable new marker reflecting early immunological conditions accompanying the tumor microenvironment establishment. Acknowledgements: grants GAAV IAA500200917, CZ.1.05/2.1.00/03.0124 (Project ExAM), RVO 61388971, RVO 67985904 (CZ), Rusconi Foundation, Varese (IT), ENI Czech Republic, Prague (CZ), Manghi Czech Republic s.r.o, Prague (CZ), Unicredit Bank s.r.o., Prague (CZ), Torino-Praga Invest and Rivergate s.r.o Prague (CZ), SIAD Czech spol. s.r.o., Prague (CZ)