Proteomics and immunohistochemistry were used to reveal tumor heterogeneity among urothelial papillomas (UPs) with the long-term goal of predicting their biological potential in terms of outcome. First, we identified proteins that were deregulated in invasive fresh lesions as compared to normal urothelium. Twenty-two major proteins showing variations of two-fold or more in at least one third of the invasive lesions were selected. A panel consisting of antibodies against CKs 5, 13, 18 and 20 and markers of squamous metaplasia (CKs 7, 8 and 14) was used to probe normal urothelium and 30 UPs collected during a period of five years. Four UPs showed a normal staining phenotype, while the rest could be grouped in 5 major types, that with the exception of type 1, shared aberrant staining with the CK20 antibody. UPs exhibited only one major type of heterogeneity that in most cases included variants. Type 1 heterogeneity (n=4) showed preferred staining of the umbrella cells with the CK8 antibody. Type 2 (n=11) was typified by the staining of the basal and intermediate layers with the CK20 antibody. Type 3 (n=7) was characterized by the predominant staining of the basal cell layer with the CK5 antibody. Type 4 (n=1) showed areas of CK7 negative cells, while type 5 (n=3) showed loss of staining of the basal cells with the CK20 antibody. 29% of the patients experienced recurrences but none progressed to invasive disease. The number of recurrences was higher in the case of types 3 and 5 (4/7 and 2/3, respectively), and all recurrent type 3 lesions progressed to a higher degree of dedifferentiation. Even though a long-term prospective study involving a larger sample size will be required to assess the biological potential of these lesions, we believe that this approach will prove instrumental for revealing cancer heterogeneity.