The effect of different intensities of the ectoparasitic salmon lice (Lepeophtheirus salmonis) on stress, growth and the expression of immune and wound healing transcripts in the skin of Atlantic salmon (Salmo salar) was investigated. Lice infection success and survival were similar at the chalimus and preadult stage in the low and high dose group, but infection success and survival were significantly lower in the high than in the low dose group at the adult stage. The expression of investigated transcripts was not correlated to lice intensities, but several of them were significantly differently expressed locally in the skin at the site of lice attachment in infected fish compared to controls. This included an up-regulation of pro-inflammatory markers at the site of lice attachment (e.g., interleukin 1-beta, interleukin 8 and the acute phase protein serum amyloid A), a reduction of markers of adaptive immunity (cluster of differentiation 8-alpha and immunoglobulin M) and decreased expression of the anti-inflammatory cytokine interleukin 10.