As a result of the diversity of lymphoid structures in the head and neck, we analyzed clinical characteristics and outcomes of 87 consecutive children with non-Hodgkin's lymphoma (NHL) arising in this region to determine if the nodal versus extranodal primary site influences prognosis. Thirty-one children had primary nodal NHL whereas 56 had extranodal NHL. The two groups were similar in the distribution of age, gender, race, serum lactic dehydrogenase levels, and disease stage. However, extranodal tumors were slightly more likely to have small non-cleaved cell histology (32/56 versus 11/31, p = 0.07) than nodal tumors. In a multivariate analysis, extranodal involvement (p = 0.017), advanced stage disease (p = 0.054) and treatment era (p = 0.056) were each significantly associated with a shorter time of event-free survival. Children with extranodal and extralymphatic NHL had an even worse treatment outcome than did others (p = 0.006). The poor prognosis of extranodal involvement was also evident among children with stage I or II NHL. We conclude that extranodal involvement has an adverse influence on treatment outcome in children with NHL arising in the head and neck region.