Progression of lung disease is a major event in children with cystic fibrosis (CF), but regional differences in its evolution are unclear. We hypothesized that regional differences occur beginning in early childhood. We examined this issue by evaluating 132 patients followed in the Wisconsin Neonatal Screening Project between 1985 and 2010. We scored chest x-rays obtained every 1–2 years with the Wisconsin chest x-ray system, in which we divided the lungs into quadrants, and gave special attention to ratings for bronchiectasis (BX) and nodular/branching opacities. We compared the upper and lower quadrant scores, and upper right and left quadrant scores, as patients aged using a multivariable generalized estimation equation (GEE) model. We did a confirmatory analysis for a subset of 81 patients with chest computerized tomography (CT) images obtained in 2000 and scored using the Brody scoring system. The chest x-ray analysis shows that the upper quadrants have higher BX (p<0.001) and nodular/branching opacities (p<0.001) scores than the lower quadrants. CT analysis likewise reveals that the upper quadrants have more BX (p=0.02). Patients positive for mucoid PA showed significantly higher BX scores than patients with nonmucoid PA (p= 0.001). Chest x-ray scoring also revealed that the upper right quadrant has more BX (p< 0.001) than the upper left quadrant, and CT analysis was again confirmatory (p< 0.001). We conclude that pediatric patients with CF develop more severe lung disease in the upper lobes than the lower lobes in association with mucoid PA infections and also have more severe lung disease on the right side than on the left side in the upper quadrants. A variety of potential explanations such as aspiration episodes may be clinically relevant and provide insights regarding therapies