Viral protein 3 (VP3) of chicken anaemia virus (CAV), also known as apoptin, has been investigated as a potent anti-cancer therapy in human. The problem in selection of the most potent apoptin is the availability of more than 800 sequence data of apoptin of CAV in GeneBank. Here we compare the apoptin of all available CAV sequences. All sequence data were downloaded from GenBank in September 9, 2024. The sequences were aligned using Mega 11 software. Consensus residues was generated using Geneious Prime software. Protein database analysis and Protein structure prediction of consensus peptide compared to putative sequence with the four most prevalence substitutions were conducted using online software Phyre 2. Overall mean distance was 0.005. Out of 121, there were 27 conserved residues. The four most common substitutions, listed from most frequent, were S67N, L25S, V73A, and C118R, which occurred in 91, 51, 34, and 32 sequences, respectively. The artificial apoptin with four of the most frequent substitutions has additional alpha-helix structure at its carboxy terminus. There was no N-link glycosylation pattern in the consensus peptide, but emerged in few isolates. Many O-link glycosylation patterns spread across the all sequences. The phosphorylation pattern of SXXXXTP, has been located in the amino- and carboxy termini of consensus peptide, while TPXXXXXR in amino terminus of apoptin. To date, the whole apoptin should be chosen with intact phosphorylation and glycosylation motives prior to the delineation of the most effective sequence demonstrating potent anti-cancer apoptosis.