When flying with pets, many animal welfare organizations strongly recommend that the pets travel in the cabin area of the aircraft with you, rather than in the cargo hold. Although the statistics on animal loss and death as a result of cargo hold shipping indicate that less than 5,000 animals are killed or lost every year in the United States, you do not want your pet to become a statistic. For this reason, if you own a small animal such as a cat, small dog, or rodent, you should make arrangements for the pet to fly in the cabin. If your animal is too large to fit in the cabin, you may want to consider an alternate mode of transportation instead of flying with pets.

When traveling in the cargo hold, pets can be subjected to temperature extremes which may include excessive heat or freezing. For this reason, many airlines do not permit pets in the cargo hold during the summer when travelers try flying with pets, as pets have been known to die in the intense heat of the closed hold while planes wait to taxi down the runway. In a cargo hold with imperfect climate control, the hold can also reaching freezing temperatures very quickly once the aircraft is in flight, which could be fatal for your pet. It is also possible for the cargo hold to lose pressure, and some cargo holds have imperfect air circulation systems, meaning that your animal has a chance of suffocating from lack of oxygen.

Traveling with pets can be very stressful; flying with pets is even more stressful for the animal. Animals do not understand the rapid temperature and pressure changes which can occur, even in the cabin of an airplane, and the stress may adversely affect the breathing and heart rate of your pet. If you are flying with pets in the cabin, you can keep an eye on their vital signs, but if the pets are isolated in the cargo hold, they may reach a state of crisis without anyone being aware of it. When flying with pets, you should also not use tranquilizers or nervous system depressants, which may cause respiratory collapse or heart failure if the animal becomes stressed in the air.

In addition to death, loss is also an issue when flying with pets, especially if you are forced to transfer. Pets are viewed as luggage or cargo by most airlines, rather than living beings, and your animal's carrier may be handled roughly during transfers, adding to the emotional and physical stress that your animal feels. In addition, the cage may end up among the millions of pieces of luggage lost annually around the world. In the United States alone, roughly six out of every 1,000 pieces of luggage is lost. If your pet is lost, the airline may offer financial compensation, but this will not compensate you for the loss of a friend.

If you absolutely must ship a pet as cargo, animal welfare activists recommend that you consider using the services of a professional live cargo shipping firm. These firms handle your animals with care and respect in aircraft specially fitted out for animal transportation. The aircraft includes medical staff to watch your animal, and the cabin is climate controlled and pressurized. Because the firm specializes in animal handling, your animal is also far less likely to be a victim of animal cruelty at the hands of an exhausted or irritable baggage handler, an unfortunate result of flying with pets on crowded airlines.