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Abstract Background The World Health Organization Disability Assessment Schedule 2.0 12-item survey (WHODAS-12) is a questionnaire developed by the WHO to measure functioning across health conditions, cultures, and settings. WHODAS-12 consists of a subset of the 36 items of WHODAS-2.0 36-item questionnaire. Little is known about the minimal important difference (MID) of WHODAS-12 in persons with chronic low back pain (LBP), which would be useful to determine whether rehabilitation improves functioning to an extent that is meaningful for people experiencing the condition. Our objective was to estimate an anchor-based MID for WHODAS-12 questionnaire in persons with chronic LBP. Methods We analyzed data from two cohort studies (identified in our previous systematic review) conducted in Europe that measured functioning using the WHODAS-36 in adults with chronic LBP. Eligible participants were adults with chronic LBP with scores on another measure as an anchor to indicate participants with small but important changes in functioning over time [Short-form-36 Physical Functioning (SF36-PF) or Oswestry Disability Index (ODI)] at baseline and follow-up (study 1: 3-months post-treatment; study 2: 1-month post-discharge from hospital). WHODAS-12 scores were constructed as sums of the 12 items (scored 0–4), with possible scores ranging from 0 to 48. We calculated the mean WHODAS-12 score in participants who achieved a small but meaningful improvement on SF36-PF or ODI at follow-up. A meaningful improvement was an MID of 4–16 on ODI or 5–16 on SF36-PF. Results Of 70 eligible participants in study 1 (mean age = 54.1 years, SD = 14.7; 69% female), 18 achieved a small meaningful improvement based on SF-36 PF. Corresponding mean WHODAS-12 change score was − 3.22/48 (95% CI -4.79 to -1.64). Of 89 eligible participants in study 2 (mean age = 65.5 years, SD = 11.5; 61% female), 50 achieved a small meaningful improvement based on ODI. Corresponding mean WHODAS-12 change score was − 5.99/48 (95% CI − 7.20 to -4.79). Conclusions Using an anchor-based approach, the MID of WHODAS-12 is estimated at -3.22 (95% CI -4.79 to -1.64) or -5.99 (95% CI − 7.20 to -4.79) in adults with chronic LBP. These MID values inform the utility of WHODAS-12 in measuring functioning to determine whether rehabilitation or other health services achieve a minimal difference that is meaningful to patients with chronic LBP.