Rabbits, guinea pigs, hamsters and other small animals are herbivores and are natural browsers of grasses and other fibrous materials. It is the fiber in their diet that drives their digestive tract and keeps it healthy. One of the most common reasons small animals develop digestive tract problems is from a diet too low in fiber or too high in carbohydrates or starches.
Fiber is typically supplied by feeding a non-legume hay such as timothy or brome hay. Hay should be fed daily, free choice. Hay should be clean, dry, and sweet smelling. Alfalfa hay is a legume hay, therefore high in protein. Feeding pellets (which are typically also a good source of protein) and alfalfa hay provides an excess of protein to the digestive tract and leaves it deficient in fiber. Alfalfa hay should be restricted to young, growing animals.
If your pet has a tendency towards bladder stones or excess urine crystal production he should be fed a diet that is low in calcium. As alfalfa is high in calcium, choose a pellet brand that is timothy based, and remove all the high calcium vegetables (parsley, lettuce, carrot tops, etc.) and alfalfa hay from the diet.
One of the most common reasons small animals are ill is due to digestive tract problems. In some cases, the damage caused to the digestive tract is permanent, in other cases; the problem needs to be addressed via extensive medical or surgical intervention.