Background: Negative pressure wound therapy with instillation (NPWTi) is an established wound conditioning tool. Previous investigations discovered that the rinsing fluid is a suitable monitoring tool containing various cells and cytokines. Methods: The aim of this pilot study was to analyze rinsing fluid samples from patients treated with NPWTi and link them to the clinical course, including microbiological contamination. In 31 consecutive patients with acute and chronic wounds, laboratory analysis was performed to evaluate IL-6, IL-8, bFGF, Tnf-a, and VEGF. Results: IL-6 showed a significant increase to 1540 pg/mL on day two and 860 pg/mL on day four (p = 0.01 and p = 0.04, resp.). IL-8 steadily increased from a median of 2370 pg/mL to a maximum of 19,400 pg/mL on day three (p = 0.01). The median bFGF showed a steady decline from 22 pg/mL to 10 pg/m (p = 0.35) on day three. The median Tnf-a increased from 11 pg/mL to 44 pg/mL (p = 001). The median VEGF values fluctuated but showed an overall increase from 35 pg/mL to 250 pg/mL (p = 0.07). Regarding IL-8, diabetic and non-diabetic patients both showed a gradual increase with non-significant higher median values for the diabetics. The subgroup analysis of IL-6 showed increasing and higher values in cases with bacterial superinfections (p = 0.07). Conclusion: We were able to use an established wound conditioning tool to gather important information about the inflammatory response during NPWTi treatment. Cytokine and cell courses were mostly consistent with the literature, especially in diabetic patients, and should be further investigated.