Flow cytometry measures multiple characteristics of single cells. The use of flow cytometry in the veterinary clinical laboratory has increased considerably during the past decade. The most common applications of flow cytometry in small animal oncology are measurement of DNA content in tumours and immunophenotyping of haematopoietic malignancies. DNA ploidy and S-phase rate of various tumours in dogs have been found to be independent predictor of patient outcome. In dogs with lymphomas immunophenotyping is recommended as a part of the patient work-up. Flow cytometry has shown to be a suitable method for immunophenotyping of canine lymphomas. However, it has not become a routine technique in small animal oncology yet. This report reviews the applications of flow cytometry in small animal oncology. Besides basic principles and technical aspects, the clinical relevance of DNA-analysis and immunophenotyping are discussed.