The Science of Acupuncture
There are theories that the insertion of needles affect certain types of nerve fibres and through that mechanism stimulate or shut down areas of the limbic system. This modulates hormones and neurotransmitters and helps pain control or restoration of homeostasis (the state of dynamic physiological balance our bodies attempt to maintain). It is certain that there are physiological effects from needling acupuncture points as opposed to other areas. Many studies show this, from changed electrical resistance, alterred blood flow in the brain and releases of hormones and neurotransmiters.
What is unclear is how these measurable changes relate to clinical effects, and doubt arises as there are many studies showing no statistically significant difference from a control form of needling. There are however many studies that do show significant differences also, there is discussion as to why this is on the research page.
There is also new work being done looking into the connective tissue network and fascia which connects and supports all tissues in the body suggesting that perhaps acupuncture relieves constrictions in this network which has reflex and possibly neurochemical effects at distant sites. some studies have shown a high anatomical correlation between fascial planes and intersections and acupuncture channels and points. See the work of Robert Schleip at the Fascia institute in Ulm and Helene Langevin at McGill university in Vermont.
In addition a significant amount of acupuncture point locations are at places where different connective tissue planes meet, meaning that affecting that tissue could transmit information of mechanical affects along multiple planes affecting multiple muscles and other tissues. There is also a significant (one study finds 80%) correlation between acupuncture points and common trigger point locations. A look at the histology of acupuncture point sites also finds some to be local to lymph nodes and neural junctions, thus possibly stimulating the immune system.
Essentially though there is not yet a completely satisfactory model for how acupuncture works according to western physiological theory though I believe we will come to an understanding some day.