Context: Qualitative methodologies are relatively new in health sciences education research, especially in the area of problem-based learning (PBL). A key advantage of qualitative approaches is the ability to gain in-depth, textured insights into educational phenomena. Key methodological issues arise, however, in terms of the strategies of inquiry, data collection methods, and analytical approaches. This review aims to identify and appraise the current applications of qualitative studies in PBL and indicate possible new methodological directions. Methods: Two computerized databases, Educational Resources Information Center (ERIC) and PubMed, were screened for solely qualitative studies of PBL in health sciences education between 2000 and 2015. Selected articles were grouped for systematic description, critical analysis, and evaluation, with a key focus on identifying methodological trends. Results: The number of recent qualitative research studies of PBL in health sciences education is small but growing, with 61 solely qualitative articles identified in the review period. Four main research issues in PBL were identified for qualitative investigation: (1) participants' experiences or perceptions; (2) facilitation; (3) assessment; and (4) educational technologies. Participants' experiences or perceptions of PBL have drawn the most research attention to date. Methodological approaches included: self-reported studies using interview data (n = 29); studies analyzing video recordings of PBL tutorials (n = 9); introspective studies analyzing written reflections (n = 6); and studies using multiple qualitative methods (n = 17). Of the 61 identified studies, the majority are perception studies, with only a limited number focused on PBL processes or interactional analyses. Conclusions: This review presented and analyzed current practices in qualitative studies of PBL in health sciences education and indicated new directions. Research designs are expanding beyond an initial focus on post-hoc perception studies to explore innovative, in situ qualitative inquiries and methodologies.