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Abstract Background Clinical practice guidelines have become increasingly widely used to guide quality improvement of clinical practice. Qualitative research may be a useful way to improve the quality and implementation of guidelines. The methodology for qualitative evidence used in guidelines development is worthy of further research. Methods A comprehensive search was made of WHO, NICE, SIGN, NGC, RNAO, PubMed, Embase, Web of Science, CNKI, Wanfang, CBM, and VIP from January 1, 2011 to February 25, 2020. Guidelines which met IOM criteria and were focused on clinical questions using qualitative research or qualitative evidence, were included. Four authors extracted significant information and entered this onto data extraction forms. The Appraisal of Guidelines for Research and Evaluation (AGREE II) tool was used to evaluate the guidelines’ quality. The data were analyzed using SPSS version 17.0 and R version 3.3.2. Results Sixty four guidelines were identified. The overall quality of the guidelines was high (almost over 60%). Domain 1 (Scope and Purpose) was ranked the highest with a median score of 83% (IQ 78–83). Domain 2 (Stakeholder involvement) and Domain 5 (Applicability) were ranked the lowest with median scores of 67% (IQ 67–78) and 67% (IQ 63–73) respectively. 20% guidelines used qualitative research to identify clinical questions. 86% guidelines used qualitative evidence to support recommendations (mainly based on primary studies, a few on qualitative evidence synthesis). 19% guidelines applied qualitative evidence when considering facilitators and barriers to recommendations’ implementation. 52% guideline developers evaluated the quality of the primary qualitative research study using the CASP tool or NICE checklist for qualitative studies. No guidelines evaluated the quality of qualitative evidence synthesis to formulate recommendations. 17% guidelines presented the level of qualitative research using the grade criteria of evidence and recommendation in different forms such as I, III, IV, very low. 28% guidelines described the grades of the recommendations supported by qualitative and quantitative evidence. No guidelines described the grade of recommendations only supported by qualitative evidence. Conclusions The majority of the included guidelines were high-quality. Qualitative evidence was mainly used to identify clinical questions, support recommendations, and consider facilitators and barriers to implementation of recommendations’. However, more attention needs to be paid to the methodology. For example, no experts proficient in qualitative research were involved in guideline development groups, no assessment of the quality of qualitative evidence synthesis was included and there was lack of details reported on the level of qualitative evidence or grade of recommendations.