AIM: The use of biomarkers of osteoarthritis (OA) have potential for early diagnosis, evaluation of disease severity and monitoring treatment. Serum and synovial fluid YKL-40 levels are increased in severe knee OA. Pulsed electromagnetic field (PEMF) therapy is a novel treatment method for OA. However, studies evaluating the PEMF therapy in treatment of knee OA revealed conflicting results. This study was conducted to objectively assess the effect of PEMF therapy in patients with knee OA, by using ultrasonographic measurements and a novel biomarker, YKL-40. METHODS: Forty patients were randomized into two treatment groups. Both groups received conventional physical therapy, while Group 1 received additional PEMF therapy. The patients were asked to rate their pain on a visual analogue scale (VAS) and complete a Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) questionnaire. Serum YKL-40 levels were measured, and knee effusion and cartilage degeneration level were evaluated with ultrasonography before and after treatment. RESULTS: Pre-treatment YKL-40 level was correlated with WOMAC pain subscale (P = 0.032, r = 0.339). VAS and WOMAC scores significantly improved in both treatment groups (P < 0.05). The effusion in the right knee significantly decreased in Group 1. The change in YKL-40 level was not correlated with the change in VAS, WOMAC scores and knee effusion. CONCLUSION: This study revealed that adjuvant PEMF therapy has no additional effect on pain in patients with knee OA. Serum YKL-40 level seems to be unuseful for monitoring the treatment in knee OA.