The Coulter STKS and the Sysmex NE-1500 were evaluated for their performance in paediatric samples. Special attention was paid to the ability of both instruments to detect white blood cell morphology abnormalities. Therefore a population with a high frequency of pathologies was selected. The studied population included children aged between 1 month and 14 years, 45% of which suffered from oncological and/or haematological diseases. Two hundred and forty blood samples were analysed. The leukocyte differentiation results from the Coulter STKS and the Sysmex NE-1500 were compared with the manual microscopic method. The differentials compared very well for neutrophils, lymphocytes and eosinophils. Sensitivity and specificity for the detection of blasts, immature granulocytes, left shift and atypical lymphocytes were examined. While specific morphology flagging showed a rather low sensitivity, blasts and immature granulocytes were mostly detected by the two systems, taking into account white blood cell alarm flags other than the two mentioned above. The overall sensitivity for the detection of white blood cell abnormalities was better with the Coulter STKS, whereas the Sysmex NE-1500 showed a higher specificity. In an ancillary study which was performed exclusively on neonatal samples, of which 80% originated from preterm infants, we found a limited sensitivity for the detection of low percentages of nucleated red blood cells for both analysers. The high frequency of abnormalities, together with the limited sensitivity mentioned above, prompted us to review all neonatal samples in the future.