We compared three neurophysiological methods for assessing small nerve fiber function in 40 patients with peripheral neuropathy to determine the various manifestation types of peripheral small fiber neuropathy. Heart rate variation tests were used to assess cardiac parasympathetic small fiber function. Cutaneous vasoconstrictor responses (sympathetic C fibers) induced by deep inspiration were examined with laser Doppler flowmetry. Cutaneous afferent C fiber function was assessed by measurement of axon reflex vasodilatation induced by histamine iontophoresis. All test parameters were significantly lower in patients with peripheral neuropathy than in control subjects. Comparison of the three small fiber systems revealed that functionally different systems are damaged independently, and isolated affection of each fiber type was frequently observed. The three tests are useful noninvasive tools with which to evaluate sympathetic, parasympathetic, and afferent small fiber function in patients with peripheral neuropathy. In many patients functionally different small fiber systems are affected selectively. To diagnose small fiber neuropathy and to evaluate the individual type of manifestation complementary testing of several small somatic and autonomic fiber systems is necessary.