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The health of honey bees is threatened by multiple factors, including viruses and parasites. We screened 557 honey bee (<i>Apis mellifera</i>) colonies from 155 beekeepers distributed all over Belgium to determine the prevalence of seven widespread viruses and two parasites (<i>Varroa</i> sp. and <i>Nosema</i> sp.). Deformed wing virus B (DWV-B), black queen cell virus (BQCV), and sacbrood virus (SBV) were highly prevalent and detected by real-time RT-PCR in more than 95% of the colonies. Acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV) and deformed wing virus A (DWV-A) were prevalent to a lower extent (between 18 and 29%). Most viruses were only present at low or moderate viral loads. Nevertheless, about 50% of the colonies harbored at least one virus at high viral load (>10⁷ genome copies/bee). <i>Varroa</i> mites and <i>Nosema</i> sp. were found in 81.5% and 59.7% of the honey bee colonies, respectively, and all <i>Nosema</i> were identified as <i>Nosema ceranae</i> by real time PCR. Interestingly, we found a significant correlation between the number of <i>Varroa</i> mites and DWV-B viral load. To determine the combined effect of these and other factors on honey bee health in Belgium, a follow up of colonies over multiple years is necessary.