Bladder cancer (BC) is one of the most common human malignancies that account for major death in the world. Apoptin that is derived from chicken anemia virus (CAV) has displayed tumor-specific cytotoxic activity in a variety of human carcinomas. However, the magical function of apoptin in bladder carcinoma cell lines has not been identified yet. In our study, we delivered apoptin into bladder-originating T24, EJ, and HCV29 cell lines by adenovirus system. The selective cytotoxic effect of apoptin was determined by cell viability assay, active caspase-3 measurement, and annexin V/PI double staining. Importantly, we have examined the differential expression patterns of tumor-associated genes including Ki67, C-erbB-2, Rb, and nm23 by flow cytometry and western blot in vitro. In an animal study, apoptin was infused into animal models by AAV system, and immunohistochemistry and quantitative real-time PCR (qRT-PCR) were employed to validate results in vivo. The results indicated that apoptin could selectively induce apoptosis in bladder tumorigenic cells coupled with tumor-specific nucleus accumulation in vitro. Interestingly, apoptin could downregulate expression levels of Ki67 and C-erbB-2 and upregulate the expression of Rb both in vitro and in vivo. Moreover, the animal models treated with AAV-apoptin have shown smaller tumor volumes and displayed better prognosis than controls. In conclusion, apoptin could selectively induce apoptosis in bladder tumor cells through altering expression profiles of tumor-associated genes.