A cross-sectional study was carried out in Galicia, NW Spain, in order to estimate the magnitude of honey bee colony losses and to identify potential risk factors involved. A total of 99 samples from 99 apiaries were collected in spring using simple random sampling. According to international guidelines, the apiaries were classified as affected by colony loss or asymptomatic. Each sample consisted of worker bees, brood and comb-stored pollen. All worker bees and brood samples were analysed individually in order to detect the main honey bee pathogens. Moreover, the presence of residues of the most prevalent agrotoxic insecticides and acaricides was assessed in comb-stored pollen. The general characteristics of the apiaries and sanitary information regarding previous years was evaluated through questionnaires, while the vegetation surrounding the apiaries sampled was assessed by palynological analysis of comb-stored pollen. The colony loss prevalence was 53.5% (CI 95% =43.2-63.9) and Nosema ceranae was found to be the only risk factor strongly associated with colony loss. The decision tree also pointed out the impact of the Varroa mite presence while variables such as apiary size, the incorrect application of Varroa mite treatments, and the presence of Acarapis woodi and Kashmir bee virus (KBV) were identified as possible co-factors.Additional key words: colony collapse; Apis mellifera; Nosema ceranae; Varroa destructor; imidacloprid; fipronil; comb-stored pollen.Correspondence should be addressed to Aránzazu Meana Mañes: ameana@ucm.es (Tables S1, S2 and S3) accompanies the paper on SJAR's website.