A method of diagnosing galactosemia in blood samples from neonates by determining GAL-1-P concentrations before 5-7 days of life is disclosed. The removal of interfering compounds allows a more specific and therefore more accurate determination of GAL-IP levels in newborn screening for galactosemia using mass spectrometry. This is of major importance when investigating samples from children that have not yet achieved a steady state of GAL-IP (i.e. before 5-7 day of life).