Considering that changes in exercise routines might have relevance in treatment of adolescents with type 1 diabetes mellitus, we sought to assess whether spontaneous modifications to weekly exercise habits might occur in these patients and whether such variations would be accompanied by alterations in autonomic profile. In this observational study, we examined 77 patients (age 15.0 ± 0.6 years.) who in addition to a tailored optimal insulin treatment were invited to perform at least 1 h a day of moderate, aerobic exercise, as suggested by recent guidelines. Patients were studied at baseline (T0) and after 15.8 ± 0.7 months (T1). They were divided into three subgroups according to increased, unchanged and diminished total estimated weekly METs between T0 and T1. Autonomic profile was evaluated by assessing spontaneous baroreflex gain and low-frequency oscillation in arterial pressure, using spectral analysis of RR and systolic arterial pressure time series. Insulin therapy and biochemical data were similar among the 3 groups at T0 and T1, while body mass index standard deviation score was slightly reduced (p < 0.04) and markers of autonomic performance were improved (alpha index, from 17 ± 1 to 20 ± 2 ms/mmHg, p < 0.002) in the group who increased the amount of exercise (from 1627 ± 250 to 3582 ± 448 METs min wt(-1), p < 0.001). Furthermore, the change in total weekly METs significantly correlates with changes of key indices of autonomic regulation. The favourable autonomic effects of moderate increase in spontaneous exercise load suggest testing more formally this intervention in adolescents with type 1 diabetes.