Validation studies of electrical impedance tomography (EIT) based assessment of regional ventilation under pathological conditions are required to prove that EIT can reliably quantify heterogeneous ventilation distribution with sufficient accuracy. The objective of our study was to validate EIT measurements of regional ventilation through a comparison with xenon-multidetector-row computed tomography (XeCT) in an animal model of sub-lobar lung injury. Nine anesthetized mechanically ventilated supine pigs were examined before and after the induction of lung injury in two adjacent sub-lobar segments of the right lung by saline lavage or endotoxin instillation. Regional ventilation was determined in 32 anteroposterior regions of interest in the right and left lungs and the ventilation change quantified by difference images between injury and control. Six animals were included in the final analysis. Measurements of regional ventilation by EIT and XeCT correlated well before (rs = 0.89 right, rs = 0.90 left lung) and after local injury (rs = 0.79 and 0.92, respectively). No bias and narrow limits of agreement were found during both conditions. The ventilation decrease in the right injured lung was correspondingly measured by both modalities (5.5%±1.1% by EIT and 5.4%±1.9% by XeCT, p = 0.94). EIT was inferior to clearly separate the exact anatomical location of the regional injuries. Regional ventilation was overestimated (<2%) in the most ventral and dorsal regions and underestimated (2%) in the middle regions by EIT compared to XeCT. This study shows that EIT is able to reliably discern even small ventilation changes on sub-lobar level.