This study was performed to determine whether genetic polymorphisms within the human papillomavirus (HPV) can predict the disease course in patients with recurrent respiratory papillomatosis. The HPV type and genomic variations were determined by comparing the sample sequence to a prototypical HPV in the database of the National Center for Biotechnology Information. The results were correlated with the clinical course. Seven children and 6 adults were studied. Six of the 7 children had aggressive disease associated with HPV type 11. The remaining child had HPV type 6. Five of the 6 adult patients had HPV type 6; 1 had a history of juvenile recurrent respiratory papillomatosis. The remaining adult had an aggressive disease course associated with HPV type 11. The HPV type and specific polymorphisms were conserved over time in serial isolates. The age of onset and medical therapy did not appear to affect the polymorphisms present. Future studies may find that the presence of certain polymorphisms is associated with different geographic locations and possibly with the disease course.