An organ pipe is a sound-producing element of the pipe organ that resonates at a specific pitch when pressurized air (commonly referred to as wind) is driven through it. Each pipe is tuned to a note of the musical scale. A set of organ pipes of similar timbre comprising the complete scale is known as a rank; one or more ranks constitutes a stop.

Organ pipes are generally made out of either metal or wood. Very rarely, glass, porcelain, plastic, paper, Papier-mâché, or even stone pipes may be seen. A historical organ in the Philippines has pipes made exclusively of bamboo.

Metal pipes are usually made of lead; for increased rigidity it is alloyed with tin along with trace amounts of antimony and copper. The percentage of each metal in the alloy influences the characteristics of the resulting pipe. A high proportion of tin results in a slightly brighter colour (optical colour, not timbre). In addition, high amounts of tin give a gleaming and long-lasting polish, which may be desired if the pipe is clearly visible. The cost of each metal is also a factor, as tin is more expensive than lead. Cost considerations may also lead to the use of the inferior rolled zinc especially for the lower tones that take a lot of material. In addition, pipes have been made of many metals, including copper, aluminium, gold electroplate, silver, brass, and iron.

Metal pipes are generally made by first casting the desired lead alloy onto a long flat surface. Once the metal cools, it is cut into pieces, which are then rolled into shapes around molds called mandrels and soldered together. Thus, the cross-section of a metal pipe is usually circular. The low melting point, solderability and malleability of the organ metal makes the construction of pipes relatively easy.

The body of a wooden pipe can be made of either a coniferous wood (softwood) or hardwood, although the lower section of the pipe (comprising the metal foot (on some pipes), cap, block and mouth) will nearly always be made from hardwood to provide a precise edge for the pipe's mouth. Using screws and glue, the pipes are assembled from wooden pieces of various shapes and sizes. In contrast with the circular cross-section of a metal pipe, the cross-section of a wooden pipe is most commonly square or rectangular.

Glass pipes have been created using warm glass and stained glass techniques by Xaver Wilhelmy. Three Wilhelmy glass ranks exist in the United States, two in a private collection in West Virginia and one in a private collection in Virginia. The image at left shows the Wilhelmy American Flag Glass Pipe Organ that was created as a part of a Memorial Proposal for Ground Zero after the events of September 11, 2001.

The bodies of organ pipes are generally made in three shapes: cylindrical, conical, or rectangular. Cylindrical pipes are simple cylinders, while conical pipes are in the shape of a tapering or expanding cone. Rectangular pipes form cuboid shapes with either a square or rectangular cross-section when viewed from above. There are some irregular shapes as well: the Flûte triangulaire, for example, has a triangular cross-section when viewed from above. In addition, a cylindrical or rectangular pipe can be tapered: that is, it can be made to be wider at the bottom than at the top. The internal shape of the pipe is a major factor in tone color.

The end of the pipe opposite the reed or mouth may be either open or closed (also known as stopped). A closed flue pipe with a uniform cross-section sounds an octave lower than a similar open pipe of the same length. Also, such an open pipe produces a tone in which both the even-numbered and the odd-numbered partials are present, while a stopped pipe, such as a gedackt, produces a tone with odd-numbered partials. The tone of a stopped pipe tends to be gentler and sweeter than that of an open pipe, though this is largely at the discretion of the voicer.