The aim of this study was to investigate the role of serum cytokines in the diagnosis of acute appendicitis (AA) and acute mesenteric lymphadenitis (AML). Data were collected prospectively on 7 to 18 year old children (October 2010 - October 2013): 31 patients with AA, 26 patients with AML, and 17 patients with elective non-inflammatory surgical disease were selected as controls. Serum levels of IL-10, IL-12(p70), IL-1β, IL-4, IL-6, IL-8, IL-17, MCP-1, EGF, TNF-α were measured. Patients with AA had significantly increased serum levels of IL-6(1) (z = -3.72; p = 0.0002) and IL-10(1) (z = -2.81; p = 0.005) compared to AML before any treatment. The consecutive measurements of MCP-1 in serum demonstrated a significant difference within 72 hours in the AA group (Wilks’ Lambda test 0.80; F(2;29) = 3.5; p = 0.04) and also in the AML group (Wilks’ Lambda test 0.70; F(2;24) = 5.0; p = 0.01). The increased values of IL-6 and IL-10 were the most reliable cytokines one hour before surgical intervention for patients with AA. MCP-1 values changed significantly within 72 hours after patient hospitalisation but did not differ between the groups, and could not be a helpful serum biomarker in distinguishing patients with AA and AML.