BackgroundChronic fatigue (CF) reflects an imbalance of inter-organ functions or of the four essential physiological components qi, blood (xue), yin, and yang. CF can be subdivided into different patterns. However, there are no diagnostic methods for CF. This study aimed to clinically validate a pattern identification method by identifying correlations between CF and responses to the qi blood yin yang deficiency questionnaire (QBYY-Q).MethodsParticipants were recruited between May and June 2014 through the Kyung Hee University Korean Medicine hospital website and via posters and comprised 129 CF patients diagnosed with the United States Centers for Disease Control and Prevention (1994) criteria. Participants who had organic diseases that explained the CF were excluded. A total of 159 participants were asked to complete the QBYY-Q, the fatigue severity scale, and the Chalder fatigue scale. The latter two questionnaires were used to assess convergent validity with the QBYY-Q. Among the 129 CF participants, 70 and 59 had chronic fatigue syndrome and idiopathic chronic fatigue, respectively. Two Korean medical doctors independently assessed participants’ qi, blood, yin, and yang deficiency patterns using QBYY deficiency pattern identification guidelines. Based on the results of a preliminary study of the QBYY-Q, we selected 32 reliable items for symptoms corresponding to each deficiency pattern. The items were used to estimate internal consistency and construct validity. Multinomial logistic regression analysis was performed for scores on each deficiency pattern.ResultsThe data were means and standard deviations or numbers of participants and proportions for continuous and categorical variables, respectively. A statistical significance level of P < 0.05 was assumed. The QBYY-Q showed satisfactory internal consistency. Explanatory factor analysis extracted two factors for each deficiency pattern. The percentages of explained variance for qi, blood, yin, and yang deficiency were 45.1, 58.0, 52.2, and 63.4 %, respectively. Each QBYY-Q deficiency score was positively associated with each corresponding deficiency pattern. Qi deficiency was used as a reference category. Odds ratios of blood, yin, and yang deficiency were 10.97, 10.69, and 14.64, respectively.ConclusionThe QBYY-Q was suitable for estimating the influences of qi, blood, yin, and yang deficiencies in CF.Trial registration This trial was registered with the Korean Clinical Trial Register (KCT0001199)Electronic supplementary materialThe online version of this article (doi:10.1186/s13020-016-0092-y) contains supplementary material, which is available to authorized users.