The chicken anaemia virus protein 3 (VP3 or apoptin) induces apoptosis specifically in tumour and transformed cells but not in normal cells. This selective apoptosis is ideal for therapeutic purposes. However, VP3, a heterologous protein, is immunogenic in vivo. Such a drawback limits its clinical usage. To diminish its potential immunogenicity, we modified the sequence of VP3. The VP3 genes functional sequence starts at 33 AA (amino acids) from the N-terminal side, and the first protein structural domain consists of 30 AA. We found that the first domain of VP3 contains no functional sequences. Therefore, this domain was removed to test whether its absence affects apoptosis. Transfection of EGFP (enhance green fluorescent protein)-modified-VP3 or HA-modified-VP3 in bladder cancer cell lines (EJ) resulted in its expression, successful localization to the nucleus and efficient induction of apoptosis. Expression of EGFP-modified-VP3 or HA-modified-VP3 had no influence on mouse fibroblast cells (3T3). The modified VP3 (30–121), like the wild-type VP3, induced EJ cell apoptosis without affecting 3T3 cells. This study increases our understanding of modified VP3 (30–121) as a possible substitute for the wild-type VP3, which makes VP3 (30–121) an interesting candidate for the development of novel therapeutic strategies.