From breeding to racing, respiratory diseases and affections are some of the most frequent problems encountered by horses, with important welfare consequences and a significant impact on the equine industry. Prevention is the most efficient way to avoid and/or to mitigate respiratory pathologies. When available, vaccination would provide protective immunity, based on stimulation of a specific immune response designed to target and neutralise the foreign agent at the mucosal level. When immunological interventions are not available, or non-adapted, prevention relies on measures that aim to reduce the risk of contact with the causative agent, seconded by an innate mucosal immunity, the first and most important line of defence until development of a specific adaptive immune response. However, such immune responses may come at a price and a fine balance between stimulation and regulation is necessary to avoid tissue damage due to uncontrolled and unspecific inflammatory and/or immune responses. These elements will be briefly presented and reviewed through specific examples of (non-)infectious agents. Due to its extent and duration, the current European equine influenza (EI) epidemic will also be reviewed in details. Despite high EIV-specific immune coverage reaching up to 90% in some specific horse groups and the use of an EI vaccine fully updated according to the last OIE recommendation on EI vaccine strain composition (i.e. EI vaccines should contain representative EIV strains of both Florida Clade 1 and Clade 2 sub-lineages, FC1 and FC2, respectively), the absence of clinical EI observed in France since mid-2015 came to an end in early December 2019. Numerous EI outbreaks were reported since in several European countries (Belgium, Germany, Ireland, the Netherlands, Sweden and the United Kingdom). The scale, number and duration of this epidemic has not been experienced in Europe since the late 1970s and 80s (as an example, horse races were shut down in the UK for 6 days in February, a measure that was last required to prevent EI dissemination in 1979). Sequencing results reveals that H3N8 EIV strains at the origin of these 2018-19 outbreaks belong to the FC1 sub-lineage, which was not isolated in France since 2009 and was usually circulating in North and South Americas. While several amino acids mutation were identified in the HA, it is not clear yet if this epidemic is linked to a mismatch with the EI vaccine strains or the introduction of a more pathogenic strains. A few anecdotal reports of EI induced mortality in the field in several EU countries and observation of mild but noticeable clinical signs of disease in EI vaccinated horses raise a question about the pathogenicity of the current FC1 EIV strain. Surveillance results highlight a larger amount of French EI outbreaks involving vaccinated horses, which is not entirely surprising when the high EI vaccine coverage measured here is taken into account. For the few cases where serum were obtained at the onset of disease, it appears that infection could be explained in half of the cases by a lower than expected SRH antibody titre at the time of contact with EIV (irrespective of the time since last immunisation). However, it is very important to note that all known field and veterinary reports indicate that clinical signs of disease observed in EI vaccinated horses were clearly reduced when compared with unvaccinated animals, which continue to support the benefit of EI vaccination.