The objective of the present investigation was to describe and localize autonomic dysfunction in acute and chronic stages of complex regional pain syndrome (CRPS). Patients were investigated twice: the first investigation was performed as soon as diagnosis was established during the acute stage of CRPS and the second investigation was performed about 2 years later. Twenty-one patients completed the follow-up investigation. The median duration of CRPS was 5 (range 2–21) weeks at first investigation and 94 weeks (22–148) at follow-up. Skin temperature was recorded by thermography, sudomotor function was assessed by thermoregulatory sweat test (TST) and quantitative sudomotor axon reflex test (QSART). Skin temperature was warmer on the affected side at the first investigation (P<0.001) and colder at follow-up (P<0.02) compared with the contralateral limb. Sudomotor output was enhanced after both TST (P<0.005) and QSART (P<0.05) at the first investigation on the affected side. However, at follow-up, sweating after TST was still increased (P<0.04) while QSART responses were not different between the affected and unaffected limbs. As compared to controls there was no statistically significant difference, neither in skin temperature nor sweating, neither on the affected nor on the unaffected side. In conclusion, the present investigation proved that vasomotor and sudomotor control are substantially altered in CRPS. In the acute stage vasomotor control is decreased in the affected limb whereas sudomotor function is enhanced. This may be the result of disturbances of thermoregulation, but different secondary peripheral mechanisms, concerning vasomotor and sudomotor function, contribute to clinical presentation of CRPS and affect autonomic function at all stages of CRPS.