This study examines the internal microstructure evolution of porcine brain during mechanical deformation. Strain rate dependency of porcine brain was investigated under quasi-static compression for strain rates of 0.00625, 0.025, and 0.10 s(-1). Confocal microscopy was employed at 15, 30, and 40% strain to quantify microstructural changes, and image analysis was implemented to calculate the area fraction of neurons and glial cells. The nonlinear stress-strain behavior exhibited a viscoelastic response from the strain rate sensitivity observed, and image analysis revealed that the mean area fraction of neurons and glial cells increased according to the applied strain level and strain rate. The area fraction for the undamaged state was 7.85 ± 0.07%, but at 40% strain the values were 11.55 ± 0.35%, 13.30 ± 0.28%, and 19.50 ± 0.14% for respective strain rates of 0.00625, 0.025, and 0.10 s(-1). The increased area fractions were a function of the applied strain rate and were attributed to the compaction of neural constituents and the stiffening tissue response. The microstructural variations in the tissue were linked to mechanical properties at progressive levels of compression in order to generate structure-property relationships useful for refining current FE material models.