Comparative effectiveness reviews (CERs) are systematic reviews that evaluate evidence on alternative interventions to help clinicians, policy makers, and patients make informed treatment choices. Reviews should assess harms and benefits to provide balanced assessments of alternative interventions. Identifying important harms of treatment and quantifying the magnitude of any risks require CER authors to consider a broad range of data sources, including randomized controlled trials (RCTs) and observational studies. This may require evaluation of unpublished data in addition to published reports. Appropriate synthesis of harms data must also consider issues related to evaluation of rare or uncommon events, assessments of equivalence or noninferiority, and use of indirect comparisons. This article presents guidance for evaluating harms when conducting and reporting CERs. We include suggestions for prioritizing harms to be evaluated, use of terminology related to reporting of harms, selection of sources of evidence on harms, assessment of risk of bias (quality) of harms reporting, synthesis of evidence on harms, and reporting of evidence on harms.