Background: Depression is common in primary care and clinicians are encouraged to screen their patients. Metaanalyses have evaluated the effectiveness of screening, but two author groups consistently reached completely opposite conclusions. Methods: We identified five systematic reviews on depression screening conducted between 2001 and 2009, three by Gilbody and colleagues and two by the United States Preventive Task Force. The two author groups consistently reached completely opposite conclusions. We analyzed two contemporaneous systematic reviews, applying a stepwise approach to unravel their methods. Decision points were identified, and discrepancies between systematic reviews authors justification of choices made were recorded. Results: Two systematic reviews each addressing three research questions included 26 randomized controlled trials with different combinations in each review. For the outcome depression screening resulting in treatment, both reviews undertook meta-analyses of imperfectly overlapping studies. Two in particular, pooled each by only one of the reviews, influenced the recommendations in opposite directions. Justification for inclusion or exclusion of studies was obtuse. Conclusion: Systematic reviews may be less objective than assumed. Based on this analysis of two meta-analyses we hypothesise that strongly held prior beliefs (confirmation bias) may have influenced inclusion and exclusion criteria of studies, and their interpretation. Authors should be required to declare a priori any strongly held prior beliefs within their hypotheses, before embarking on systematic reviews.