The purpose of the experiment was to compare apoptosis induced by equine influenza virus (EIV A1 and EIV A2) infection in MDCK, RK13, and NEURO-2A cell lines. Flow cytometry was used to observe two symptoms of apoptosis: phosphatidylserine translocation in plasmalemma (annexin V assay) and the fragmentation of DNA generated by endonuclease activity (TUNEL assayterminal deoxynucleotidyl transferase biotin-dUTP nick end labelling). The differences in the onset of apoptosis in the studied cells was observed. In MDCK cells infected with EIV A1 and A2, a weak signal of the phosphatidylserine translocation was observed but more cells showed the DNA fragmentation. An opposite effect was observed in case of RK 13 cells. NEURO-2A cells displayed a similar number of annexin V and TUNEL positive cells after the infection with EIV A2, while in case of EIV A1 infection, only the early symptoms of apoptosis were noted. Differences between both viral serotypes could originate from functioning of viral proteins responsible for induction or inhibition of apoptosis. The differences between cell types may result from the activation of cellular pro or anti-apoptotic mechanisms.