The molecular defects underlying haemoglobinopathies are both deletions and point mutations in the alpha- or beta-globin genes or gene-clusters. To detect point mutations causing alpha- or beta-thalassaemia, direct sequencing is the method of choice to detect the widest spectrum of molecular defects. The most established approach in DNA diagnostics to screen for the most common deletion defects causing alpha-thalassaemia or beta-thalassaemia is gap- PCR, Multiplex Ligation-dependent Probe Amplification (MLPA) and Sanger Sequencing technology to detect breakpoint sequences of previously uncharacterized deletions/duplications. We demonstrate the recent advances in the determination of duplications and deletions causing alpha- or beta-thalassemia, using Next Generation Sequencing, array Comparative Genome Hybridization and Target Locus Amplification. We present three cases in which the use of advanced technologies allow the diagnosis of unexpected disease genotypes.