The present study was part of a larger surveillance effort to identify the determinants of African honey bee health, and, particularly, to detect honey bee pathogens across Kenya, where 160 colonies were examined from 32 apiaries (five colonies/apiary). From each colony, 20 individual foragers, nurse bees, worker pupae, and drone pupae were sampled separately. These were organized as 30 foragers, 32 nurse bees, 28 worker pupae, and 10 drone pupae pools. Nucleic acid was extracted from the pooled homogenates and tested using a panel of 18 different (RT-)PCR methods targeted at detecting Paenibacillus larvae, Melissococcus plutonius, Ascophaera apis, Aspergillus spp., Nosema ceranae, N. apis, Deformed wing virus (DWV), Varroa destructor virus 1 (VDV 1), Acute bee paralysis virus (ABPV), Sacbrood virus (SBV), Israeli acute paralysis virus (IAPV), Black queen cell virus (BQCV), Chronic bee paralysis virus (CBPV), and Kashmir bee virus. All amplified bands were sequenced and compared to the GenBank database. VDV 1 was the most abundant virus at 50% prevalence in the 100 bee pools. It was closely followed by DWV at 44%. The others were BQCV (36%), SBV (14%), IAPV (9%), ABPV (8%), and N. ceranae (5%). The pathogens co-existed within apiaries. VDV 1 was present in 66% of the apiaries, DWV in 69%, BQCV in 69%, SBV in 28%, IAPV in 22%, ABPV in 19%, and N. ceranae in 13%. The study concludes that these pathogens should be incorporated in honey bee disease surveillance activities in the region.