The occurrence of dead dormant flower buds is a common phenomenon of economic importance in the major pear production areas of Europe. Thus far, the cause of dead flower buds disease remained unknown. Several causes have been proposed, including insufficient tree chilling, unmet dormancy requirements, incompatibility between scion and cultivar, but also various biotic stress agents such as pathogens and pests. In this study, we tested the relationship between reduction of tree growth and dead flower bud incidences, but found no indication that growth regulation can prevent the occurrence of dead flower buds. It has been proposed that the bacterium Pseudomonas syringae pv. syringae may be the causal agent of dead flower buds of pear. However, although we found the bacterium as epiphyte and even as endophyte on and in flower buds, our findings argue that P. syringae pv. syringae is not the causal agent of dead flower buds disease in the Netherlands. In our research, Alternaria spp. were consistently found in diseased flower buds, and strong correlations between dead dormant flower buds and infection rates of flower buds with Alternaria spp. were recorded. The isolated Alternaria species were identified as A. arborescens SC and A. alternata SC. Field experiments for disease control showed that the disease may be controlled by specific fungicide applications. Thus, we propose that dead flower buds of pear in the Netherlands should be regarded as a fungal disease caused by A. alternata SC and potentially also A. arborescens SC.