The antimicrobial activity of nineteen organic acids and two monoacylglycerols in cultures of Campylobacter jejuni CCM 6214T was determined using a SYBR Green-based real-time PCR assay. Caprylic, capric and lauric acids were the most efficient antimicrobials among the compounds tested (IC50 ≤ 0.10 mg/ml). Antimicrobial activity of organic acids was pH-dependent, being more pronounced at a lower pH than at a pH higher than 6. In the cells treated with capric acid, fumaric acid and monocaprin, the permeability of the cytoplasmic and outer membrane was measured using potassium ion-selective and tetraphenylphosphonium (TPP+)-selective electrodes, respectively. The effect of capric and fumaric acids on morphological status of C. jejuni cells was further studied using transmission electron microscopy. The results show that antimicrobial activity of organic acid against C. jejuni is variable and supplementation of feeds with some acids may have insufficient effects.