Infectious diseases, due to their massive scale, are the greatest pain for all rabbit breeders. Viral infections cause enormous economic losses in farms. Treating sick rabbits is very difficult and expensive, so it is very important to prevent disease by vaccinating. In order to successfully fight viral infections, it is important to know about the immune response of an infected animal. The aim of this study was to analyze the immune response mediated by antimicrobial peptides (myeloperoxidase (MPO) and lysozyme (LZM)) in peripheral blood neutrophils and rabbit serum by non-invasive immunological methods. The study was carried out on mixed breed rabbits that were experimentally infected with two strains (Erfurt and Rossi) of the Lagovirus europaeus/GI.1a virus. It has been observed that virus infection causes changes in the form of statistically significant increases in the activity of MPO and LZM concentration, while in the case of LZM activity only statistically significant decreases were noted. Additionally, clinical symptoms typical for the course of the disease were noted, and the probability of survival of the animals at 60 h p.i. (post infection) was 30% for the Erfurt strain, and −60% for the Rossi strain. The obtained results of MPO and LZMs suggest that these enzymes, especially MPO, may serve as a prognostic marker of the state of the immune system of rabbits.