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Objectives Autoanalyzers are used in clinical haematology for analysis of blood samples in clinical as well as in nonclinical studies. The results from these analyzers vary from machine to machine. In this study, we compared the lymphocyte and neutrophil count of mouse blood between ADVIA 2120i, Horiba Yumizen H2500 and CellaVision analyzers against manual counting as gold standard. Methods Blood samples from 28 female BALB/c mice were collected and analyzed. Agreement between different autoanalyzers and manual counting were determined by Bland–Altman method. Results A high level of agreement was found between CellaVision and manual technique for lymphocyte (Bias=4.75, 95% limits of agreement −14 to 24) and neutrophil count (Bias=0.68 (−17 to 19)). Agreement in lymphocyte count was also observed between ADVIA and manual counting, but to a lesser extent compared to CellaVision (Bias=13.9 (−10.45 to 38.27)). However, no agreement was observed for ADVIA (Neutrophils), Horiba (lymphocytes and neutrophils) with manual counting. Conclusions Our data suggests that CellaVision could be used for the differential counting of neutrophil and lymphocytes in mouse blood sample.