Lymphocyte counts in patients with leptospirosis have been shown to be variable. This study retrospectively compared lymphocyte counts from the first blood samples taken following hospital presentation in patients with leptospirosis who were either (i) IgM non-reactive, (ii) IgM reactive and microscopic agglutination test (MAT) non-reactive or (iii) IgM and MAT reactive in an effort to determine whether differences in lymphocyte counts are observed in the acute and immune phase of leptospirosis. Statistical differences in lymphocyte counts were observed between the three groups. In conclusion, this study has shown that the phase of leptospiral infection may affect patient lymphocyte counts.