Chicken is cooked when it reaches the temperature necessary to denature (break down) most proteins, which kills any salmonella or other disease-causing agents and changes the texture of the meat.

The juices that come out of meat as it cooks should be fat or water, both of which are colorless, but they could pick up color from the materials they pass through, such as the hemoglobin protein that gives muscle tissue its pink or red color. I suspect the denaturing of the proteins prevents them from leaking out, thus the juices become clear. Once the hemoglobin has been broken down, you can safely assume that the proteins that pathogens rely on to survive have been destroyed as well. So yes, the color of the juices coming from inside the meat should be a reliable indicator of doneness.

SIDEBAR: There are in fact a few bacterial spores that can survive to much higher temperatures, as can the toxic chemicals produced as a waste product of some bacteria. These are relatively rare, and can be easily avoided by eating fresh, clean food and refrigerating any leftovers promptly.

EDIT addressing @Aaronut's comment: Most bacteria that live in, on, and around plants and animals require the same fairly narrow temperature range. 165 degrees F is enough to reliably kill salmonella and just about any standard pathogen (anything that would thrive inside the human body) in a minute or so, by also denaturing many of the proteins that make up the bacteria's cell walls and internals. This site suggests that 165 F is also the temperature at which juices will run clear - so yes, if the juices are running clear, the pathogens should already be dead, and probably for the same reason.

ANOTHER SIDEBAR: In fact, poultry can be cooked at a much lower temperature if you're sufficiently careful. 40 minutes at 140 degrees is just as effective at killing salmonella. (I don't know whether this would also make the juices run clear, but I would guess so.) The catch is that in a traditional oven, there's no way to get the middle of the chicken that hot for 40 minutes without drying out the outside. Sous-vide cooking addresses this by cooking smaller pieces of food at very precise temperatures for long periods of time. The FDA publishes charts indicating how long you need to cook at a given temperature to

Chicken is cooked when it reaches the temperature necessary to denature (break down) most proteins, which kills any salmonella or other disease-causing agents and changes the texture of the meat.

The juices that come out of meat as it cooks should be fat or water, both of which are colorless, but they could pick up color from the materials they pass through, such as the hemoglobin protein that gives muscle tissue its pink or red color. I suspect the denaturing of the proteins prevents them from leaking out, thus the juices become clear. Once the hemoglobin has been broken down, you can safely assume that the proteins that pathogens rely on to survive have been destroyed as well. So yes, the color of the juices coming from inside the meat should be a reliable indicator of doneness.

SIDEBAR: There are in fact a few bacterial spores that can survive to much higher temperatures, as can the toxic chemicals produced as a waste product of some bacteria. These are relatively rare, and can be easily avoided by eating fresh, clean food and refrigerating any leftovers promptly.

EDIT addressing @Aaronut's comment: Most bacteria that live in, on, and around plants and animals require the same fairly narrow temperature range. 165 degrees F is enough to reliably kill salmonella and just about any standard pathogen (anything that would thrive inside the human body) in a minute or so, by also denaturing many of the proteins that make up the bacteria's cell walls and internals. This site suggests that 165 F is also the temperature at which juices will run clear - so yes, if the juices are running clear, the pathogens should already be dead, and probably for the same reason.

ANOTHER SIDEBAR: In fact, poultry can be cooked at a much lower temperature if you're sufficiently careful. 40 minutes at 140 degrees is just as effective at killing salmonella. (I don't know whether this would also make the juices run clear, but I would guess so.) The catch is that in a traditional oven, there's no way to get the middle of the chicken that hot for 40 minutes without drying out the outside. Sous-vide cooking addresses this by cooking smaller pieces of food at very precise temperatures for long periods of time. The USDA publishes charts indicating how long you need to cook poultry at a given temperature to destroy bacteria at specified levels of lethality.

Chicken is cooked when it reaches the temperature necessary to denature (break down) most proteins, which kills any salmonella or other disease-causing agents and changes the texture of the meat.

The juices that come out of meat as it cooks should be fat or water, both of which are colorless, but they could pick up color from the materials they pass through, such as the hemoglobin protein that gives muscle tissue its pink or red color. I suspect the denaturing of the proteins prevents them from leaking out, thus the juices become clear. Once the hemoglobin has been broken down, you can safely assume that the proteins that pathogens rely on to survive have been destroyed as well. So yes, the color of the juices coming from inside the meat should be a reliable indicator of doneness.

*SIDEBAR: There are in fact a few bacterial spores that can survive to much higher temperatures, as can the toxic chemicals produced as a waste product of some bacteria. These are relatively rare, and can be easily avoided by eating fresh, clean food and refrigerating any leftovers promptly.

Chicken is cooked when it reaches the temperature necessary to denature (break down) most proteins, which kills any salmonella or other disease-causing agents and changes the texture of the meat.

The juices that come out of meat as it cooks should be fat or water, both of which are colorless, but they could pick up color from the materials they pass through, such as the hemoglobin protein that gives muscle tissue its pink or red color. I suspect the denaturing of the proteins prevents them from leaking out, thus the juices become clear. Once the hemoglobin has been broken down, you can safely assume that the proteins that pathogens rely on to survive have been destroyed as well. So yes, the color of the juices coming from inside the meat should be a reliable indicator of doneness.

SIDEBAR: There are in fact a few bacterial spores that can survive to much higher temperatures, as can the toxic chemicals produced as a waste product of some bacteria. These are relatively rare, and can be easily avoided by eating fresh, clean food and refrigerating any leftovers promptly.

EDIT addressing @Aaronut's comment: Most bacteria that live in, on, and around plants and animals require the same fairly narrow temperature range. 165 degrees F is enough to reliably kill salmonella and just about any standard pathogen (anything that would thrive inside the human body) in a minute or so, by also denaturing many of the proteins that make up the bacteria's cell walls and internals. This site suggests that 165 F is also the temperature at which juices will run clear - so yes, if the juices are running clear, the pathogens should already be dead, and probably for the same reason.

ANOTHER SIDEBAR: In fact, poultry can be cooked at a much lower temperature if you're sufficiently careful. 40 minutes at 140 degrees is just as effective at killing salmonella. (I don't know whether this would also make the juices run clear, but I would guess so.) The catch is that in a traditional oven, there's no way to get the middle of the chicken that hot for 40 minutes without drying out the outside. Sous-vide cooking addresses this by cooking smaller pieces of food at very precise temperatures for long periods of time. The FDA publishes charts indicating how long you need to cook at a given temperature to