Molecular diagnostics have an increasing impact on diagnosis, risk stratification and targeted treatment in haemato-oncology. In the framework of a pilot study for the implementation of next-generation sequencing in the Belgian healthcare system, the Commission of Personalised Medicine was founded to give professional and evidence-based advice on the molecular analysis in haemato-oncology. This paper describes its recommendations for NGS analysis in myeloid malignancies. In addition, the minimally required set of genes that must be analysed is defined and algorithms for molecular workflow in myeloid malignancies are proposed.