They usually rest near or inside their burrows during midday. Pygmy rabbits may be active at any time of day however, they are generally most active at dusk and dawn. Juvenile mortality was highest from birth to 5 weeks of age. Green & Flinders (1980) reported a maximum estimated annual adult mortality of 88% in Idaho. The mortality of adults is highest in late winter and early spring. Young from early litters grow larger due to a longer developmental period prior to their first winter. The growth rates of juveniles are dependent on the date of birth. It is unlikely that litters are produced in the fall. In Idaho the third litter is generally produced in June.

An average of six young are born per litter and a maximum of three litters are produced per year. It is between 27 and 30 days in various species of cottontails ( Sylvilagus spp.). The gestation period of pygmy rabbits is unknown. In Idaho it lasts from March through May in Utah, from February through March. The breeding season of pygmy rabbits is very short. Pygmy rabbits are capable of breeding when they are about 1 year old.

A crossbreeding program conducted by the Oregon Zoo, Washington State University, and Northwest Trek is attempting to preserve the genetic line by breeding surviving females with the Idaho pygmy rabbit. The last male purebred Columbia Basin pygmy rabbit, found only in the Columbia Basin of Washington state, died 30 March 2006, at the Oregon Zoo in Portland. An isolated population occurs in east-central Washington, and another in Wyoming. Distribution continues west to southern Idaho and southern Oregon, and south to northern Utah, northern Nevada, and north-eastern California. Pygmy rabbits are found in southwestern Montana from the extreme southwest corner near the Idaho border north to Dillon and Bannack in Beaverhead County. The range of the pygmy rabbit includes most of the Great Basin and some of the adjacent intermountain areas of western North America. The pygmy rabbit is distinguishable from other leporids by its small size, short ears, gray color, small hind legs, and lack of white fuzzy fur. The pygmy rabbit is the world's smallest leporid, with adults weighing between 375 and 500 grams (0.827 and 1.102 lb), and having a body length between 23.5 and 29.5 centimeters (9.3 and 11.6 in) females are slightly larger than males. Historically, the pygmy rabbit has also been placed in the genera Microlagus and Sylvilagus. erected the new subgenus Brachylagus for the pygmy rabbit Brachylagus has since been elevated to the rank of genus. The pygmy rabbit was first described by Clinton Hart Merriam in 1891, as Lepus idahoensis the type specimen, in winter pelage, had been collected in the Pahsimeroi Valley the previous autumn.

Federal government, though the International Union for Conservation of Nature lists the species as lower risk. One isolated population, the Columbia Basin pygmy rabbit, is listed as an endangered species by the U.S. The pygmy rabbit differs significantly from species within either the Lepus (hare) or Sylvilagus (cottontail) genera and is generally considered to be within the monotypic genus Brachylagus. It is also the only native rabbit species in North America to dig its own burrow. The pygmy rabbit ( Brachylagus idahoensis) is a rabbit species native to the United States. Lepus idahoensis Merriam, 1891 Lepus (Brachylagus) idahoensis Microlagus idahoensis

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