The multidrug resistance gene 1(MDR1) expression levels were analysed in 27 dogs with different types of malignant lymphomas receiving a standard chemotherapy protocol. Blood samples were used for MDR1 real-time PCR expression analysis. Treatment tolerance and outcome were evaluated on a regular basis by clinical examination and client questioning. Dogs developing severe adverse effects under treatment showed significantly lower basal MDR1 gene expression levels when compared with those who tolerated the drugs well. In the longitudinal MDR1 gene expression analysis during treatment, four dogs showed a greater than two-fold MDR1 up-regulation, compared to baseline expression. All four of these dogs, but none of the others, showed disease progression. In conclusion, basal and follow-up MDR1 gene expression levels could be of predictive value for the occurrence of severe adverse drug reactions and/or the development of MDR during chemotherapy for lymphoma in dogs.