The concept of a dojo as a martial arts training place is a Western concept; in Japan, any physical training facility, including professional wrestling schools may be called dojos as well depending on the context.

Martial arts dōjō

A proper Japanese martial arts dōjō is considered special and is well cared for by its users. In many styles it is traditional to conduct a ritual cleaning of the dōjō at the end of each training session (called souji, which translates from Japanese as "cleaning"). Besides the obvious hygienic benefits of regular cleaning it also serves to reinforce the fact that dojo are supposed to be supported and managed by the student body, not the school's instructional staff. This attitude has become lost in many modern, commercial dōjō that are founded and run by a small group of people or instructors. In fact, it is not uncommon that in traditional schools (koryu), dōjō are rarely used for training at all, instead being reserved for more symbolic or formal occasions. The actual training is conducted typically outdoors or in a less formal area.

Many traditional dōjō follow a prescribed pattern with shomen ("front") and various entrances that are used based on student and instructor rank laid out precisely. Typically students will enter in the lower-left corner of the dōjō (in reference to the shomen) with instructors in the upper right corner. Shomen typically contains kamidana—an area for a Shintō shrine and other artifacts. The term kamiza is frequently confused by martial arts practitioners with the Kamidana. Many other artifacts may be displayed throughout the dōjō, such as kanban that authorize the school in a style or strategy, and items such as taiko drums or armor (yoroi). It is not uncommon to find the name of the dōjō and the dōjō kun (roughly "dōjō rules") displayed prominently at shomen as well. Visitors also typically have a special place reserved, depending on their rank and station. Weapons and other training gear will normally be found on the back wall.

A fine example of a traditional kendō dōjō is Noma dojo in Tokyo.

A hombu dōjō or honbu dōjō of a style is considered the administrative and stylistic headquarters or a particular martial arts style or group. This does not necessarily mean that they are large or ostentatious.

Some well-known hombu dōjō located in Japan are:

• Kodokan
• Aikikai hombu dojo
• Bujinkan Hombu Dojo

in Zen Buddhism

Dōjō is also used to describe the meditation halls where Zen Buddhists practice zazen meditation. It is sometimes used instead of the term "zendo" which is more specific, and more widely used. European Soto Zen groups affiliated with the International Zen Association prefer to use "dōjō" instead of zendo to describe their meditation halls as did their founding master, Taisen Deshimaru.