Currently, there is some confusion and misinformation surrounding the use of alfalfa hay and timothy hay for rabbits and even guinea pigs.

What is the difference between alfalfa hay and timothy hay?

Both hay sources are excellent forages to provide to your herbivores, but there are some differences between them nutritionally. To understand how those differences impact your animals, some background information is needed.
 

Complete diets for rabbits and other small pets 

Most diets manufactured for small pets are sold as complete diets. In other words, this diet is formulated in such a way that it can be the sole source of nutrition for your animal and no supplemental hay, veggies or other treats are needed. Providing treats in small amounts can help you bond with your pet, but overfeeding them may cause nutritional imbalances or lead to obesity. In order to manufacture a complete diet, nutritionists take into account the nutrient requirements of that species. Various ingredients are mixed together so that a diet contains the correct amount of protein, fat, fiber, vitamins and minerals required for optimal health.

Alfalfa hay and timothy hay are different nutritionally

Alfalfa hay and timothy hay are both forage sources commonly used in rabbit and guinea pig diets. Nutritionally speaking, however, they are very different. Alfalfa contains higher concentrations of protein and calcium compared to timothy hay (Table 1). When alfalfa or timothy is used in a complete rabbit feed, the nutrients of the hay source used is taken into account and mixed with other appropriate ingredients to obtain a final diet formula that meets the needs of rabbits or guinea pigs. For example, while calcium is much higher in alfalfa than in timothy, in a complete feed, the amount of additional calcium sources (such as calcium carbonate) would be lower in an alfalfa-based diet compared to a timothy-based formula.

Rabbits and calcium

Calcium metabolism in rabbits is unique compared to other species. Rabbits are efficient calcium absorbers and excrete excess calcium in their urine. For this reason, rabbit urine may leave a white, chalky residue. Because of this unique metabolic system, rabbits are prone to urinary stones if fed too much calcium. Therefore, when feeding an adult rabbit supplemental hay in addition to a complete diet, it is preferable to provide timothy hay to minimize excess calcium. 
 
Table 1. Nutrient composition of alfalfa hay and timothy hay, dry matter basis^*
 

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^* National Research Council. Nutrient requirements of small ruminants: Sheep, goats, cervids, and New World camelids. National Academies Press: 2006; Washington, DC.