Inhalation of CO2 or isoflurane is a commonly used method of euthanasia with mice, but information related to their effects on serum inflammatory markers in chronic models of inflammation is limited. In the current study, nineteen-week old DBA female mice with (n = 53) or without (n = 51) collagen-induced arthritis were randomly assigned to euthanization with CO2 (n = 55) or isoflurane (n = 49. Plasma was collected for the measurement of soluble intercellular adhesion molecule-1 (sICAM-1), tumor necrosis factor alpha (TNF-alpha), and interleukin-6 (IL-6) by ELISA. When mice without and with collagen-induced arthritis were pooled, compared to CO2, administration of isoflurane was associated with lower production of the pro-inflammatory cytokines TNF-alpha (pg/ml, mean +/- SEM) (26.1 +/- 2.82 versus 48.1 +/- 7.99) and IL-6 (25.18 +/- 2.73 versus 48.1 +/- 6.82) (ANOVA, p < 0.05). In contrast to TNF-alpha and IL-6, administration of CO2 decreased the plasma sICAM-1 level (1170+/- 50 versus 758 +/- 24 for CO2) (p < 0.00001). When data were analyzed as a function of collagen-induced arthritis, the differences between CO2 and isoflurane persisted. Low plasma sICAM-1 levels found in CO2 euthanasia group may be due to degradation. Since mice are the most common animal model for studying inflammation, researchers should be aware of these iatrogenic experimental variables before interpreting their data.