The local immune responses to swine influenza isolate of the H3N2 subtype in single infection and in co-infection with Bordetella bronchiseptica or Pasteurella multocida were analyzed using quantitative real-time PCR assays for a panel of swine cytokines. We observed that the severity of clinical signs correlated with co-infections comparing to the single H3N2 infection. The median virus titers in nasal swas between 2 and 4 DPI for H3N2, H3N2/Pm and H3N2/Bbr groups were 10^2.9 TCID50/g, 10^3.4 TCID50/g, and 10^2.8 TCID50/g, respectively. The average H3N2 virus titres expressed as TCID50/g in lungs peaked between 2 and 4 DPI in all infected groups, and there were no statistical differences in the virus titres between the challenge groups. General pro-inflammatory cytokine response in lungs was more pronounced in co-infected pigs, comparing to pigs infected with the either agent alone. H3N2 and Bbr co-infection caused a mild disease associated with a strong and rapid innate as well as with the increased viral replication. The frequency of coughing intensified after 2DPI in H3N2/Bbr groups and after 4DPI in H3N2/Pm animals. All infected animals showed intensification of clinical signs at 3DPI. H3N2 and Pm co-infected pigs revealed a strong up-regulation of IFNα, although it did not correlate with the viral replication or clinical signs. TNF-α mRNA levels were detected only in the H3N2 group and were lower than all other cytokines in all infected groups. INFα, IL-1β and IL-8 were elevated in lungs of coinfected pigs and correlated with enhanced lesions. Transcript levels of IL-10 and IL-4 did not increase at any time point in all infected animals. The obtained results suggest that viral and bacterial co-factors may interfere with the host response at early stages of a disease more efficiently, at least until 4 DPI.