A systematic review was undertaken to produce an annotated bibliography of meta-analyses in vaccinology and to evaluate their methodological quality. Based on our evaluation using the Oxman and Guyatt index, the methodological quality of the 121 meta-analyses included in this study is not satisfactory. The most frequent limitations include non-comprehensive bibliographic research; bias in the selection of the studies; lack of quality assessment of individual studies; absence of evaluation of heterogeneity among studies and publication bias. The methodological quality significantly increases with the year of publication and with declared financial support, without differences between profit and non-profit support. Meta-analyses with a higher Oxman and Guyatt quality score are more likely to include only randomized trials and to explore appropriately potential sources of heterogeneity. Most of the methodological deficiencies of meta-analyses in vaccinology could be corrected easily, and meta-analysts should improve the methodological quality of their work to maintain their impact on policy decisions.