Qualitative research is increasingly valued as part of the evidence for policy and practice, but how it should be appraised is contested. Various appraisal methods, including checklists and other structured approaches, have been proposed but rarely evaluated. We aimed to compare three methods for appraising qualitative research papers that were candidates for inclusion in a systematic review of evidence on support for breast-feeding. A sample of 12 research papers on support for breast-feeding was appraised by six qualitative reviewers using three appraisal methods: unprompted judgement, based on expert opinion; a UK Cabinet Office quality framework; and CASP, a Critical Appraisal Skills Programme tool. Papers were assigned, following appraisals, to 1 of 5 categories, which were dichotomized to indicate whether or not papers should be included in a systematic review. Patterns of agreement in categorization of papers were assessed quantitatively using kappa statistics, and qualitatively using cross-case analysis. Agreement in categorizing papers across the three methods was slight (kappa =0.13; 95% CI 0.06-0.24). Structured approaches did not appear to yield higher agreement than that by unprompted judgement. Qualitative analysis revealed reviewers' dilemmas in deciding between the potential impact of findings and the quality of the research execution or reporting practice. Structured instruments appeared to make reviewers more explicit about the reasons for their judgements. Structured approaches may not produce greater consistency of judgements about whether to include qualitative papers in a systematic review. Future research should address how appraisals of qualitative research should be incorporated in systematic reviews.