Health literacy (HL) is often discussed in the context of school curricula, however there is a lack of published and varified instruments for evaluating HL in schoolaged children in Russia. This article presents the step-by-step development of a multidimensional assessment method of health literacy (MMHL) for middle-school children. The conceptual model is based on a review of international experience of HL measurement and includes three functional sections — autonomy, motivation, and practice; and four themes — hygiene, daily routine, nutrition and physical activity. The final version of the instrument consists of 54 questions in 9 scales: access to information, beliefs, trust, amotivation, extrinsic motivation, intrinsic motivation, critical thinking, communication, and action. Work was carried out in five stages: 1) expert evaluation and verification of content validity; 2) small pilot study (N = 92) to test face validity; 3) large pilot study (N = 313) for the primary assessment of psychometric characteristics; 4) final study on a larger sample (N = 1095) to confirm the psychometric characteristics and to explore the factor structure of the instrument; 5) analysis of the distribution of test scores and the establishment of threshold values for interpreting the results. The developed instrument has good indicators of validity and reliability. The Confirmatory Factor Analysis shows that the data corresponds with the theoretical model. Threshold values allow using this instrument not only in theoretical studies but also for solving practical pedagogical tasks. Therefore this instrument can be recommended for use in educational institutions as a diagnostic tool for assessing the motivation and HL of students.