Ugandan honey bees (Apis mellifera L.) produce honey, and are key pollinators within commercial crops and natural ecosystems. Real-time RT-PCR was used to screen immature and adult bees collected from 63 beekeeping sites across Uganda for seven viral pathogens. No samples tested positive for Chronic bee paralysis virus, Sacbrood virus, Deformed wing virus, Acute bee paralysis virus, Apis iridescent virus or Israeli acute paralysis virus. However, Black queen cell virus (BQCV) was found in 35.6% of samples. It occurred in adults and larvae, and was most prevalent in the Western highlands, accounting for over 40% of positive results nationally.