Since the early 1990s the number of systematic reviews (SR) of animal studies has steadily increased. There is, however, little guidance on when and how to conduct a meta-analysis of human-health-related animal studies. To gain insight about the methods that are currently used we created an overview of the key characteristics of published meta-analyses of animal studies, with a focus on the choice of effect size measures. An additional goal was to learn about the rationale behind the meta-analysis methods used by the review authors. We show that important details of the meta-analyses are not fully described, only a fraction of all human-health-related meta-analyses provided rationales for their decision to use specific effect size measures. In addition, our data may suggest that authors make post-hoc decisions to switch to another effect size measure during the course of their meta-analysis, and possibly search for significant effects. Based on analyses in this paper we recommend that review teams: 1) publish a review protocol before starting the conduct of a SR, prespecifying all methodological details (providing special attention to the planned meta-analysis including the effect size measure and the rational behind choosing a specific effect size, prespecifying subgroups and restricting the number of subgroup analyses), 2) always use the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) checklist to report your SR of animal studies, and 3) use the random effects model (REM) in human-health-related meta-analysis of animal studies, unless the assumptions for using the fixed effect model (FEM) are all met.