A method for the in vitro differential diagnosis of thyroid diseases is described comprising the step of determining by means of mass spectrometry in a biological sample the variation in intensity of at least one of the peaks (m/z)±0.3% selected from the group consisting of 10129 Th, 9749 Th, 10092 Th, 7935 Th, 4620 Th, 4748 Th, 8565 Th, 7565 Th, 4518 Th, 7936 Th, 5044 Th, 6699 Th, 11310 Th, 12277 Th, 6805 Th, 6880 Th, 8566 Th, 8309 Th, 5564 Th, 9711 Th, 7263 Th, 10296 Th and 4353 Th and/or of at least one of the peaks (m/z)±0.3% selected from the group consisting of 4987 Th, 7110 Th, 4804 Th, 9957 Th, 6719 Th, 4372 Th, 4196 Th, 4111 Th, 4282 Th, 5935 Th and 5519 Th.