Cytokines are signaling proteins that have been of significant importance in the field of immunology, since these proteins affect different cells in the immune system. In addition to their immune system significance, these proteins have recently been referred to as a third chemical communication network within the CNS. The role that cytokines play in orchestrating the immune response within tissues after a mechanical injury leads to potential complications if the source of cytokines (i.e., trauma vs disease) is of interest. Microdialysis sampling has seen wide use in collection of many different solutes within the CNS. Yet, implantation of microdialysis guide cannulas and the probes creates tissue injury. In this study, we compared the differences in cytokine levels in dialysates from 4 mm, 100 kDa molecular weight cutoff (MWCO) polyethersulfone membrane microdialysis probes implanted in the hippocampus of male Sprague− Dawley rats. Comparisons were made between animals that were dialyzed immediately after cannula implantation (day 0), 7 days post cannula implantation (day 7), and repeatedly sampled on day 0 and day 7. Multiplexed bead-based immunoassays were used to quantify CCL2 (MCP-1), CCL3 (MIP-1α), CCL5 (RANTES), CXCL1 (KC/GRO), CXCL2 (MIP-2), IL-1β, IL-6, and IL-10 in dialysates. Differences in cytokine concentrations between the different treatment groups were observed with higher levels of inflammatory cytokines measured in day 7 cannulated animals. Only CCL3 (MIP-1α), CXCL1 (KC/GRO), CXCL2 (MIP-2), and IL-10 were measured above the assay limits of detection for a majority of the dialysates, and their concentrations were typically in the low to high (10−1000) picogram per milliliter range. The work described here lays the groundwork for additional basic research studies with microdialysis sampling of cytokines in rodent CNS.