Fusarium is an emerging pathogen with high levels of morbidity and mortality. A significant tissue response is observed in infected patients, and the condition has been associated with the production of toxic metabolites. The aim of the present study was to identify a major fraction of crude metabolic extract of Fusarium oxysporum and investigate its effects on the skin of healthy rats. Fraction F1 was obtained from the cultivation of F. oxysporum in Czapek–Dox. In the treatment groups, fraction F1 (0.05 mg/ ml) was injected intradermally, while (50 µl) 0.9% of saline solution was injected in the control groups. The animals were killed 3, 6, 12, and 24 h after inoculation. The skin was fixed for inclusion in paraffin to obtain histological sections and stained with hematoxylin and eosin, Sirius red, and terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling. Samples were analyzed using Fourier transform Raman spectroscopy. The tissue reactions were classified and compared over time and by treatment. In the treatment group, inflammatory reaction peaked at 6 h, being classified as moderate, with infiltrate composed mainly of neutrophils. terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling staining was negative. The area occupied by types I and III collagen in the treatment group increased over time. There was a change in the area occupied by amide I and the ratios of the –CH2 and –CH3 molecules. It can be argued that the fraction F1 contains elements that contribute to the invasion of Fusarium in the skin, destructurizing the organization of the extracellular matrix. Copyright © 2014 John Wiley & Sons, Ltd.