Honey bee (Apis mellifera L.) colonies are subjected to many persistent viral infections that do not exhibit clinical signs. The identification of criteria that could identify persistent or latent infections in bee colonies is a challenging task for field investigators and beekeepers. With this aim in view, we developed a molecular method to estimate the viral loads for six different RNA viruses in bee and mite individuals collected from seemingly healthy colonies (360 colonies). The data showed very large viral titres in some samples (>109 copies per bee or mite). Discrepancies between adults and pupae viral RNA loads and, in several instances, significant seasonal variations among viruses were observed. The high titres of some RNA viruses recorded in mites confirm that Varroa destructor could promote viral infections in colonies.