Unique properties of X-ray fluorescent analysis with synchrotron radiation and classical morphological method allowed to reveal interrelation between the trace elements content and structure of lymph nodes. Belonging of lymph nodes to different regions is defining in formation of a certain microelemental profile and features of the microanatomic organization of lymph nodes. Lymph nodes have different functional specialization with prevalence of immune or drainage function and a certain microelement composition. The inguinal lymph node has active drainage function because of the developed sinus system at the maximum of Mn, Fe, Zn concentration; immune function prevails in a tracheobronchial lymph node at the low content of all trace elements; the mesenteric lymph node has evenly developed drainage and immune functions at the maximum of Cu, Se contents. The content of trace elements is considered as the leading mechanism limitation the structural organization of lymph nodes. Innovative approach helped to reveal formation of lymphoid-microelemental association. Features of this association modify the structural organization of lymph nodes depending on localization (region specifics).