The review deals with the progress in the diagnostics of inherited metabolic disorders by mass spectrometry in the last decade. It is focused on the atmospheric pressure ionisation techniques, i.e. electrospray ionisation and atmospheric pressure chemical ionisation. The first part of the article describes very briefly the molecular causes of inherited metabolic disorders, such as disorders of metabolisms of fatty acids, amino acids, bile acids, purine and pyrimidine and related metabolites. The other part describes the procedures from sampling over the analysis itself to the raw data evaluation.