The complete blood count analysis is of great importance in animals, as it can help in the initial diagnosis and the subsequent follow-up for these patients. For this purpose, the manual count is mainly used in rabbits to identify different cell populations and their respective percentages. Different studies have shown that complete blood count can also be performed using automatic methods to analyse rabbit cell populations. Flow cytometry is a relatively new technique in veterinary medicine that has been used for the diagnosis and staging of many medical disorders in many species. In this study, sixty-one peripheral blood samples were collected from healthy rabbits and analysed using both classic manual method and flow cytometry to evaluate the usefulness of flow cytometry in identifying different cell populations based only on their scatter properties. The results showed that flow cytometry is a reliable method to detecting different cell populations, such as granulocytes, small and large lymphocytes (for all: intra-class correlation coefficient >0.75) with high accuracy based on their scatter properties. Biases calculated using the Bland-Altman approach ranged from -0.1118to -1.256 for large lymphocytes and monocytes, respectively. However, further research with a larger number of cases and the implication of other helping techniques such as cell sorting, is necessary to fully confirm these results.