Acupuncture has been practiced for more than 2000 years in China and now all over the world. One core idea behind this medical practice is that stimulation at specific body regions (acupoints) can distantly modulate organ physiology, but the underlying scientific basis has been long debated. Here, I summarize evidence supporting that long-distant acupuncture effects operate partly through somato-autonomic reflexes, leading to activation of sympathetic and/or parasympathetic pathways. I then discuss how the patterning of the somatosensory system along the rostro-caudal axis and the cutaneous-deep tissue axis might explain acupoint specificity and selectivity in driving specific autonomic pathways, particularly those modulating gastrointestinal motility and systemic inflammation.