The Pseudomonas H6 lipopeptide is a surfactant which is able to eliminate various parasitic pathogens including the ciliate Ichthyophthirius multifiliis in vitro. This suggests an application for aquaculture purposes. However, further information on efficacy of the compound and possible immune modulation of surfactant exposed fish should be gathered before usage at farm level is considered. We performed an in vivo infection experiment using rainbow trout fry (mean weight 4.6 g, mean length 7.6 cm) as hosts and I. multifiliis theronts as the parasitic pathogen. We compared infection level, immune gene regulation and immune cell density in gills of 1) non-exposed control fish, 2) parasite exposed but untreated fish, 3) surfactant treated fish without parasite exposure, and 4) fish exposed both to parasites and surfactant. The surfactant concentration was 10 mg/L, the infection dosage 1000 theronts/fish and the exposure period 12 h. The parasite infection was recorded and samples were taken from rainbow trout gills at day 0 and 10 post-exposure. We performed an immunohistochemical investigation (detecting cells positive for MHC II, SAA, CD8, IgM, IgT and IgD) and measured the expression of genes encoding cathelidin-1, CD8, hepcidin, IFN γ, IgDs, IL-1β, IL-6 and SAA. Theront exposed fish (without surfactant treatment) became heavily infected whereas concomitant surfactant treatment (10 mg/l), along with parasite exposure, could prevent infection. A significant inflammation (upregulation of il-1β, il6, ifn γ, cathelicidin, hepcidin) was elicited in non-treated and parasite exposed fish but it was prevented by the surfactant treatment. When investigated 10 days after treatment no immune gene regulation was seen in fish exposed to surfactant only. The therapeutic effect may be due to a direct parasiticidal action of the surfactant, but it cannot be excluded that a modulation of the host immune reaction may influence the infection success.