Background: Low back pain (LBP) is a common health problem and a substantial part of LBP is presumed to be attributable to degeneration of the intervertebral disc. For patients suffering from intractable discogenic LBP, there are few evidence-based effective interventional treatment options available. In 2010, the results of a randomized controlled trial (RCT) were published concerning "intradiscal methylene blue injection" (IMBI), in which this intervention appeared to be very successful in relieving discogenic pain. Therefore, we decided to repeat this study to investigate whether we could replicate the published results. The results of our preliminary feasibility study gave reason to set up an RCT. The aim of this RCT is to evaluate if IMBI is a more effective treatment of discogenic low back pain as an intradiscal placebo intervention, and furthermore, to assess the cost-effectiveness of this intervention. Methods/Design: Consecutive discogenic low back pain patients referred to four specialized pain treatment facilities are being screened for eligibility. After a positive standardized provocation discography and informed consent, patients are randomized into two groups. The treatment group receives an intradiscal injection with methylene blue, lidocaine, and contrast, and the control group receives intradiscal isotonic saline with lidocaine and contrast. Main outcome measures are pain at the 6-month follow-up, patient's global impression of change, cost-effectiveness, quality of life, disability, and analgesic intake. Discussion: The importance of this study is emphasized by the fact that for intractable discogenic low back pain patients, evidence-based effective pain treatments are rare. If this study establishes clinical success and cost-effectiveness, IMBI could become the "pain treatment of choice" for a selected group of patients with chronic discogenic low back pain for whom noninvasive treatment options have failed.