Domestic horses are currently often subject to management practices that can entail social stressors, which in turn can negatively influence immunocompetence and disease susceptibility. The present study therefore aimed to characterize the number of various blood leukocyte subsets in horses, focusing on two potentially stressful housing environments: changes in group composition and relocation to individual stabling. Immune measurements were conducted before as well as one and eight days after changes were made. They were complemented by an assessment of plasma cortisol concentrations as well as behavioral observations. One and eight days after relocation to single housing, the mean numbers of eosinophils, T helper cells and cytotoxic T cells decreased by up to 31%, 20% and 22% respectively, whereas the mean numbers of neutrophils increased by 25%. In contrast, one and eight days after changes in group composition not only the mean number of neutrophils, but also of monocytes, T helper cells and cytotoxic T cells increased by up to 24%, 17%, 9%, and 15% respectively. In consequence, an increase in the neutrophil-to-lymphocyte ratio indicating stress-induced immune modulation was found after relocation to single housing, but not after changes in group composition. The changes in leukocyte numbers after relocation to single housing were accompanied by a transient increase in cortisol concentrations after one day and the occurrence of disturbed behavior patterns one week after change in housing condition. In contrast, changes in group composition did not result in an increase of cortisol concentrations or in an increase of aggressive interactions. The results strongly indicate that individual stabling is an intense stressor leading to acute and lasting alterations in blood counts of various leukocyte types. The study highlights a probable negative impact of single housing on welfare and health of horses and an advantage of group housing systems in view of immunocompetence.