Background The birth prevalence of severe haemoglobinopathies such as sickle cell disease (SCD) in the Netherlands has been estimated to be at least 50 newborns per year. Neonatal screening for SCD was added to the Dutch screening programme in January 2007. We here evaluated three high performance liquid chromatography (HPLC) systems for application in neonatal screening for haemoglobinopathies, and present the results of a subsequent pilot screening programme. Methods The Variant NewBorn Screening (Vnbs) HPLC system (Bio-Rad) was validated by analysing 131 blood samples and blood mixtures. Subsequently, the performance of the G7 (Tosoh BioScience) and Ultra (Primus Corporation) was compared with the Vnbs. The three HPLC analysers were tested in a pilot screening programme on 21,969 dried blood spot samples from the routine Dutch neonatal screening programme. Results The pilot screening resulted in 188 abnormal patterns. The three HPLC devices presented comparable within-and between-run precision and detected the abnormal samples similarly. The high throughput, sampling systems, presentation of results, and integration of the chromatograms, however, were different. Conclusion All three analysers detected the same abnormal haemoglobins satisfactorily, but integrated the chromatograms with variable imprecision. Comparison of the results suggested that the Bio-Rad Vnbs was the preferred system. However, software adjustments were required to improve the diagnostic potential of this device for screening for β- and α-thalassaemia.