This study compared the autonomic responses to an active orthostatic test and Stroop Color Word Test (Stroop) as well as cognitive performance in Stroop in twelve severely overtrained (OA, 6 men and 6 women) and twelve control athletes (CA, 6 men and 6 women). RR-intervals were recorded during the orthostatic test, the Stroop, and a relaxation period succeeding the Stroop. Low frequency power during standing in the orthostatic test was lower in OA than in CA (1322 +/- 955 ms2 vs. 2262 +/- 1029 ms2, p = 0.030, respectively). During Stroop, OA had higher relative total power (50 +/- 47 % vs. 19 +/- 14 % of the individual total power during supine rest after awakening, p = 0.028, respectively) and high frequency power (38.5 +/- 9.4 % vs. 13.5 +/- 2.3 % of the individual high frequency power during supine rest after awakening, p = 0.035, respectively) than CA. In the Stroop, OA made more mistakes than CA (9.7 +/- 6.5 % vs. 5.4 +/- 3.0 %, p = 0.045). The increase in absolute total power from the Stroop to relaxation correlated negatively with the amount of mistakes in the Stroop (r = - 0.588, p = 0.003). Thus, cardiac autonomic modulation during orthostatic task and responses to cognitive task and to relaxation, as well as the cognitive performance were attenuated in severe overtraining.