The earliest clinical sign for the diagnosis of tuberous sclerosis (TS) is the presence of cutaneous hypopigmented macules. However, there are no clinical, histopathological or functional criteria to discriminate between hipopigmented macules of TS and those without associated pathology. In this prospective study, the responses of the autonomous nervous system, erythema and sweating induced through iontophoresis with pilocarpine, were studied in three groups of patients (20 with TS, 10 with hipomelanosis of Ito, and 10 with hipopigmented macules without associated pathology). In hipopigmented macules without associated pathology, the responses were similar to those observed in normal skin. In TS erythema and sweating were significantly diminished (p = < 0.001). In hypomelanosis of Ito the decrease in erythema and sweating were not statistically significant. In TS the degree of decrease of erythema and sweating correlated positively with the severity of the neurological alterations. Light and electronmicroscopic studies of the hypopigmented macules in the three groups showed morphologically normal sweat glands and nerves. The latter suggests a disfunction of the sweat glands in TS as a cause of their abnormal behavior. We conclude that sweat testing in hypopigmented macules is a useful mean for the early diagnosis of ET.