In this paper, we present the segmentation of the headand neck lymph node regions using a new active contourbased atlas registration model. We propose to segment thelymph node regions without directly including them in theatlas registration process; instead, they are segmentedusing the dense deformation field computed from theregistration of the atlas structures with distinctboundaries. This approach results in robust and accuratesegmentation of the lymph node regions even in thepresence of significant anatomical variations between theatlas-image and the patient's image to be segmented. Wealso present a quantitative evaluation of lymph noderegions segmentation using various statistical as well asgeometrical metrics: sensitivity, specificity, dicesimilarity coefficient and Hausdorff distance. Acomparison of the proposed method with two other state ofthe art methods is presented. The robustness of theproposed method to the atlas selection, in segmenting thelymph node regions, is also evaluated.