The above question asked on google has been worth about a quarter of all the hits on my blog according to SiteMeter.
So here is some information on how the two kinds of airport scanners work:
"Backscatter X-ray is an advanced imaging technology. Traditional X-ray machines detect hard and soft materials by the variation in transmission through the target. In contrast, backscatter X-ray detects the radiation that reflects from the target. It has potential applications where less-destructive examination is required, and can be used if only one side of the target is available for examination.
The technology is one of two types of whole body imaging technologies being used to perform full-body scans of airline passengers to detect hidden weapons, tools, liquids, narcotics, currency, and other contraband. A competing technology is millimeter wave scanner. These airport security machines are also referred to as "body scanner", "whole body imager (WBI)", and "security scanner""
"The TSA has slowly been implementing the use of X-ray scanners in airports (so far, 38 airports have 206 of the machines) in order to see through passengers' clothes and check them for explosive devices. Officials have asserted that the machines are okay to use on the basis of the everyday use of X-rays in medical offices. However, a group of four UCSF professors pinpointed several important differences between the medical X-ray machines and those used in airports. They described the issues in a letter to Dr. John P. Holdren, the assistant to the president for science and technology."
"A normal X-ray image is a familiar sight—depending on the exposure, an X-rayed person typically appears only as a skeleton. This is because the X-rays used in those machines penetrate the skin and can only scatter off of the larger atoms in bones.
Unlike a medical X-ray, the TSA X-ray machines are a sci-fi fan's dream: they are lower-energy beams that can only penetrate clothing and the topmost layers of skin. This provides TSA agents with a view that would expose any explosives concealed by clothing. But according to the UCSF professors, the low-energy rays do a "Compton scatter" off tissue layers just under the skin, rather than the bone, possibly exposing some vital areas and leaving the tissues at risk of mutation."
"Because the X-rays only make it just under the skin's surface, the total volume of tissue responsible for absorbing the radiation is fairly small. The professors point out that many body parts that are particularly susceptible to cancer are just under the surface, such as breast tissue and testicles. They are also concerned with those over 65, as well as children, being exposed to the X-rays."
ars technica - FDA sidesteps safety concerns over TSA body scanners
"A millimeter wave scanner is a whole body imaging device used for airport security screening. It is one of two common technologies of full body scanner used for body imaging; the competing technology is backscatter X-ray."
"Clothing and many other materials are translucent in some EHF (millimeter wave) radio frequency bands. This frequency range is just below the (related) sub-millimeter terahertz radiation (or "T-ray") range.
The millimeter wave is transmitted from two antennas simultaneously as they rotate around the body. The wave energy reflected back from the body or other objects on the body is used to construct a three-dimensional image, which is displayed on a remote monitor for analysis."
"Millimeter wave radiation and radio frequency radiation is not genotoxic (unlike X-rays and ultraviolet radiation), but chronic exposure to lower frequencies of microwaves in some animal studies have been correlated with accelerated development of existing tumors.
A study conducted by Boian S. Alexandrov and colleagues at the Center for Nonlinear Studies at Los Alamos National Laboratory on Terahertz radiation (which is a 1000 times higher in frequency than mm waves) in New Mexico performed mathematical models how terahertz fields interact with double-stranded DNA, showing that, even though involved forces seem to be tiny, nonlinear resonances (although much less likely to form than less-powerful common resonances) could allow terahertz waves to "unzip double-stranded DNA, creating bubbles in the double strand that could significantly interfere with processes such as gene expression and DNA replication". Experimental verification of this simulation was not done and as the effect is frequency dependant the studies do not cover the mm wave region of the spectra were the whole body scanners operate."
This next article is a really good one:
"Another group of scientists at the University of California, San Francisco, sent a letter to the President's science and technology adviser arguing that the X-ray scanner poses a greater risk than medical X-rays and the radiation absorbed during a flight. In those two cases, the radiation is distributed evenly throughout the body, the doctors say. The radiation from the scanners, however, is embedded in the skin, resulting in a higher concentration of radiation in a given area.
Questions remain including how the X-ray scanners will affect frequent flyers (including businessmen and flight attendants who could go through security anywhere from 200 to 400 times a year), children, pregnant women and travelers with weakened immune systems. There is also a question of what could happen should a machine get stuck or fail, potentially blasting one point on a person's body with excess X-ray radiation.
The good news about scanners: Millimeter wave scanners, which are also in use at airports around the country, use very far infrared waves, waves at the opposite end of the electromagnetic spectrum from the dangerous ionizing radiation of X-ray waves. X-rays are shorter waves that can penetrate the skin and alter DNA. Millimeter waves, by contrast, are longer waves that penetrate clothes but stop at the skin. The millimeter scan is akin to a heat lamp and is considered to be far safer than X-ray scanners."
Physics Central - Airport Body Scanners: To Fear or Not to Fear?
PCWorld - X-Ray Body Scanner Hubbub: The Naked Truth