The word bacillus is a descriptive term for the appearance of certain bacteria when viewed microscopically. It derives from the Latin for "staff" and means "rod-shaped". A Gram stain allows one to distinguish between cocci (round) and bacilli (rod-shaped) bacteria, as well as between Gram-positive and Gram-negative bacteria (the former are stained red, the latter purple). In this sense, bacilli can be either Gram-positive or Gram-negative.

When capitalized and italicized, Bacillus is also the name given to a genus of rod-shaped, Gram positive, aerobic bacteria belonging to the family Bacillaceae among the Firmicutes.

Bacillus bacteria are ubiquitous in nature and can form roughly spherical spores when conditions are stressful in order to survive in a dormant state for extended periods. There exist a huge number of species in this genus, most of which are harmless.

The two species considered medically significant are Bacillus anthracis (which causes anthrax) and Bacillus cereus (which can cause a form of food poisoning similar to that of Staphylococcus). Two species that are notable food spoilers are Bacillus subtilis and Bacillus coagulans. B. subtilis is an obligate aerobe whose spores can survive the extreme heating which is often used to cook food. It is responsible for causing ropiness in spoiled bread. B. coagulans can grow all the way down to pH 4.2 and causes a flat sour taste in contaminated canned food (including acidic foods which normally keeps most bacterial growth to a minimum).

Bacillus are gram and catalase positive bacteria who use oxygen as their terminal electron acceptor in their energy metabolic pathway. Individual Bacillus appear as rods under the microscope with usually a substantial number of the rods having an oval endospore which tends to bulge the bacterium at one end. Colonies of this genus are usually are observed as large, spreading and irregularly-shaped.

An easy way to isolate a Bacillus species is by placing non-sterile soil in a test tube with water, shake, place in melted mannitol salts agar, and incubate at room temperature for at least a day.