Eosinophilia after allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been associated with the development of acute and chronic graft-versus-host disease (cGVHD). However, a limited number of studies have investigated the course of eosinophil counts in relation to the onset of cGVHD. In this study, the course of relative eosinophil counts (RECs) was retrospectively analyzed in 64 patients who developed cGVHD following allogeneic HSCT in relation to overall survival (OS), relapse rate and clinical course of cGVHD. At onset of cGVHD, eosinophilia was observed in 45% of the patients and developed one week prior to cGVHD diagnosis. Furthermore, a trend towards improved OS in patients with eosinophilia was observed. Beneficial effects were most evident in patients who exhibited decreasing eosinophil counts one week after diagnosis of cGVHD. By contrast, an increase in or stable eosinophil counts one week after diagnosis were associated with significantly impaired OS and a significantly higher rate of later aggravation of cGVHD. Findings of this study suggested that the course of eosinophil counts may provide a useful parameter in the assessment of cGVHD development and activity allowing the potential identification of patient subpopulations with a good outcome and reduced cGVHD-related mortality.