Water in third world countries and taken from streams or lakes my have microorganisms which can cause diarrhea (Dysentery) and or Flatulence (gas). It is caused by a sudden intestinal infection. It may be called gastroenteritis, Montezuma's Revenge, Turista, or the GI Trots.

Backcountry Hiking: The Giardia and cryptosporidium parasites and E. coli bacteria are considered to be the main problems. Viruses are infrequent.
Developing Countries: Bacteria and viruses such as Hepatitis and parasites are all common.

See more information below.

Treatments

• Boiling:
  Recommendations vary on how long you need to boil it, though 2-3 minutes is the standard advice.
  Pros: No taste, no pump, no chemicals
  Cons: Pounding scalding water is difficult
• Iodine:
  Products: Potable Aqua tablets, Polar Pure ($11)
  Pros: Cheap, lightweight, easy to use
  Cons: Bad taste, crypto will still get you
• Chlorine dioxide:
  Products: Potable Aqua and Katadyn, McNett's Aquamira
  Pros: Kills everything, simple, inexpensive, little to no flavor
  Cons: Undissolved tablets and drops extremely toxic
  
• Filters and Purifiers:
  Purifier pumps water thru a unit like a filter, but uses electrostatic attraction to remove viruses.
  Products: Many filters, First Need Deluxe Purifier ($95)
  Pros: No taste, removes sediment, tried-and-true technique
  Cons: Bulky, lots of squatting, easily clogged with sediment, expensive filter replacements, simple filters don't remove viruses because they are too small.
• UV light:
  Products: SteriPEN from Hydro-Photon ($149), AquaStar Deluxe from Meridian Design ($99)
  Pros: Fast, no flavor, kills viruses
  Cons: Expensive, bulb durability concerns, battery-powered
• Electrified Brine
  Products: MIOX from MSR ($130)
  Pros: Little to no flavor, can treat large volumes of water
  Cons: Expensive, requires disposable "testing strips"

More Information on the risk:
According to the May 2006 ACM Outdoors: "No study has ever been done on back-country water quality in the Northeast. While most experts agree that the vast majority of sources are probably safe, the consequences of acquiring an intestinal infection are not worth the risk."

A UC Davis Medical School report, "Backcountry Water Quality Tests Are Good News For Campers" in December 2004, published in Wilderness and Environmental Medicine, Vol. 15, Issue 4 says:

"Except for some heavily used areas, streams and lakes in the high country of the Sierra Nevada are generally clean and fresh. UC Davis physician Robert Derlet and pathology researcher James Carlson present data gathered from nearly 100 locations throughout the Sierra Nevada during the summer of 2003, including Yosemite, Sequoia and Kings Canyon national parks. Their goal was to analyze wilderness water quality for the presence of harmful bacteria such as E. coli, which is typically an indicator of contamination from human or animal waste.

Running counter to popular belief, the two researchers downplay the risk of picking up Giardia in backcountry drinking water. In the Sierra Nevada, E. coli and other pathogenic bacteria may pose a greater risk than Giardia for causing waterborne illnesses in people.
They quote a 1993 study "Cyst acquisition rate for Giardia lamblia in backcountry travelers to Desolation Wilderness, Lake Tahoe." by Zell SC and Sorenson SK. J Wilderness Med. 1993;4:147-154.

What's impressive is that more than half of our water sampling sites had no water quality problems whatsoever," said Derlet, a professor of emergency medicine at the UC Davis School of Medicine and an avid backpacker with 30 years of experience hiking in California's high Sierra. "People still should use water filters or purification techniques like boiling drinking water in the backcountry."

...

Lakes are typically 'cleaner' than creeks, possibly because the ultraviolet rays of sunlight work better at killing off bacteria in calm waters of a lake than in the tumbling flows of a stream; Bacteria readings appear higher at the beginning of spring runoff rather than later in the summer when water levels are lower and water quality is thought to be poorer;

Valley air pollution could be contributing to water quality problems in the Sierra Nevada.

See also:
Traveler's diarrhea (TD)
Safe water practices in the Back Country at Oregon State