Factory farming has resulted in commercial milk containing antibiotics, manure, pus as well as hormones (see also here). The US meat supply has been found to be contaminated with industrial pollutants, staph bacteria, the superbug Clostridium difficile, MRSA (see here, here), drug residues, anabolic steroids, copper, parasites, and antibiotics. And factory farmed chicken is especially loaded with fecal residue (see here, here) as well as E. coli and arsenic. Furthermore, because of the way the animals are raised (little exercise, confinement), the meat is also high in calories and fat. Even factory farmed fish may be contaminated with industrial toxins (see also here), artificial coloring, and possibly mad cow disease prions.
See also the related blog post: Supreme Court case: meat industry sues to keep downed animals in food supply
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