Brain response within contralateral S1 (cS1) to the hand that was more affected during electroacupuncture (EA) correlated with median nerve sensory latency. For carpal tunnel syndrome (CTS), activation in cS1 during EA at local acupoints was positively correlated with median nerve latency. Thus, the greater the dysfunction (i.e., slower median nerve conduction) was, the greater the activation was in cS1. For HC, activation in cS1 during EA at local acupoints was negatively correlated with median nerve latency. Thus, the greater median nerve conduction (i.e., faster median nerve conduction) was, the greater the activation was in cS1. This relationship did not exist for either CTS or healthy control (HC) during EA at distal acupoints. fMRI, functional magnetic resonance imaging; N.S., not significant; R to left of brain images, right; R in graphs, correlation coefficient.