Quantitation of lesions in large gyrencephalic brains presents a variety of technical challenges. Specific techniques are required when comparing lesions in subjects of different ages in order to assess maturational effects. We have modified existing techniques to attain reliable, consistent and reproducible paraffin-embedded histological sections for volumetric lesion analysis and correlation with magnetic resonance imaging (MRI) in piglets of different ages following focal traumatic brain injury. Twenty-four Yorkshire domestic piglets at three different ages (5 days, 1 month, and 4 months old) underwent scaled cortical impact injury to the fronto-parietal cortex. This contusion model utilizes a rapid volume of indentation scaled proportionally to the growth of the brain, allowing for examination of maturational influences on the brain's response to focal mechanical trauma. To overcome problems with differential processing and embedding of brains ranging from 43 to 107 g, we developed a piglet parallel brain slicing apparatus. Along with specific methods for processing, embedding, mounting, and slide preparation, these techniques enabled excellent quality 10-microm serial coronal sections to be obtained for histology and immunohistochemical analysis. Accurate co-registration of histologic, immunohistochemical and radiologic images at different ages was possible, which may enhance understanding of developmental aspects of brain injury pathophysiology.