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In the study current recommendations of the European Pharmacopeia and European Medicines Agency on vaccine safety evaluation in respect to adventitious contaminating agents, e.g., viral originating from biological substances used for vaccine manufacturing were presented and discussed. According current recommendations, adventitious contaminating agents testing include viral identification by in vivo and in vitro infectivity, PCR, and electron transmission microscopy. The scope of safety tests might be however not sufficient in some cases. Improvement of adventitious testing, mostly viral, might be achieved by application of newly developed and validated analyses of vaccine metagenome, and/or introduction of next generation sequencing methods, DNA microarrays, real-time PCR or mass-spectrometry. Currently, the new generation tools were found useful in the practical detection of PCV1 and PCV2 circoviruses specific DNA sequences in the content of rotaviruses vaccines. Routine application of the widen safety measures for adventitious content agents testing will rely on their approval by competent authorities.