Twenty managed honey bee colonies, split between 5 apiaries with 4 hives each, were monitored between the summer of 2011 and spring of 2013. Living bees were sampled in July 2011, July 2012, and August 2012. Twenty-five, medium-aged bees, free of varroa mites, were pooled per colony and date, to form one sample. Unlike in France and Belgium, Chronic Bee Paralysis Virus (CBPV) has not been found in Luxembourg. Slow Bee Paralysis Virus (SBPV) and Israeli Acute Paralysis Virus (IAPV) levels were below detection limits. Traces of Kashmir Bee Virus (KBV) were amplified. Black Queen Cell Virus (BQCV), Varroa destructor Virus-1 (VDV-1), and SacBrood Virus (SBV) were detected in all samples and are reported from Luxembourg for the first time. Varroa destructor Macula- Like Virus (VdMLV), Deformed Wing Virus (DWV), and Acute Bee Paralysis Virus (ABPV) were detected at all locations, and in most but not all samples. There was a significant increase in VDV-1 and DWV levels within the observation period. A principal component analysis was unable to separate the bees of colonies that survived the following winter from bees that died, based on their virus contents in summer. The number of dead varroa mites found below colonies was elevated in colonies that died in the following winter. Significant positive relationships were found between the log-transformed virus levels of the bees and the log-transformed number of mites found below the colonies per week, for VDV-1 and DWV. Sacbrood virus levels were independent of varroa levels, suggesting a neutral or competitive relationship between this virus and varroa.