Differences Between MSL and GPS Altitudes

From the article:

That the earth does not have a geometrically perfect shape is well established, and the geoid is used to describe the unique and irregular shape of the earth. However, only recently have the more substantial irregularities in the surface created by the global mean sea level (MSL) been observed. These irregularities are an order of magnitude greater than experts had predicted. Controlled by the gravitational potential of the earth, these irregularities form very gentle but massive "hills" and "valleys." This astonishing finding was made possible through the use of GPS, a technology designed by the United States Department of Defense to revolutionize navigation for the U.S. Navy and Air Force. GPS has done that—and a lot more.