The molecular genetic changes reported in bladder tumors can be classified as primary and secondary aberrations. Primary molecular alterations may be defined as those directly related to the genesis of cancer. These are frequently found as the sole abnormality and are often associated with particular tumors. There are characteristic primary abnormalities involved in the production of low-grade/well-differentiated neoplasms, which destabilize cellular proliferation but have little effect on cellular ''social'' interactions or differentiation, as well as the rate of cell death or apoptosis. Other molecular events lead to high-grade neoplasms which disrupt growth control, including the cell cycle and apoptosis, and which have a major impact on biological behavior. A primary target leading to low-grade papillary superficial bladder tumors resides on chromosome 9, while p53 gene alterations are commonly seen in flat carcinoma in situ. Other molecular alterations must be elucidated, as many non-invasive neoplasms have neither chromosome 9 nor p53 alterations. Novel approaches utilizing tissue microdissection techniques and molecular genetic assays are needed to shed further light on this subject. Secondary genetic or epigenetic abnormalities may be fortuitous, or may determine the biological behavior of the tumor. Multiple molecular abnormalities are identified in most human cancers studied, including bladder neoplasms. The accumulation, rather than the order, of these genetic alterations may be the critical factor that grants synergistic activity. In this regard, it is noteworthy that many of the genes that are altered act upon the two recognized critical growth and senescence pathways, TP53 and RB. These particular molecular aberrations may be especially important to evaluate for their use in the management of bladder cancer because of their commonality in progressive forms of the disease. Thus, clinical trials are underway to explore their use in specific situations, particularly in the surgical management of locally advanced disease, and to determine whether adjuvant chemotherapy in such patients may be of benefit. The use of molecular alterations in the management of non-invasive bladder neoplasms remains to be firmly established. Our knowledge of molecular alterations important in bladder cancer progression is far from complete, and further study is necessary to further elucidate crucial pathways involved in progression and therapeutic response. As per preneoplastic conditions, difficulties in identifying and interpreting the significance of phenotypic changes have imposed certain limitations, as has an evolving nomenclature and issues of reproducibility in interpreting morphological criteria. Nevertheless, molecular alterations involving chromosome 9q and the INK4A locus in papillary superficial tumors vs changes in chromosomes 14q and 8q, p53 and RB in flat carcinoma in situ lesions may indicate a molecular basis for early events that lead to varying pathways in urothelial tumorigenesis. Studies aimed at revealing the clinical relevance of genetic instability, as well as molecular or epigenetic alterations, in urothelium and preneoplastic lesions of otherwise morphologically normal appearance are needed to further advance knowledge in the field. Clinical advances in bladder cancer will be facilitated by novel animal models paralleling the human disease. Molecular diagnostics, particularly specific antigen expression, fluorescence in situ hybridization and microsatellite analyses, have shown great promise as screening and follow-up methodologies, and may supplement urine cytology in the diagnosis and characterization of new and recurrent disease. In addition, the use of high-throughput genomic/proteomic assays, linked to comprehensive databases, and coupled with robust bioinformatics will be key elements in elucidating the components of regulatory and signaling pathways involved in bladder tumorigenesis and cancer progression. [ABSTRACT FROM AUTHOR]