Under most circumstances, minor league teams are not owned by Major league clubs, but have affiliation contracts with them. A small number of minor league clubs are directly owned by major league clubs, but these are rare. Major league Rule 56 governs the standard terms of a Player Development Contract (PDC), which is the standard agreement of association between a minor league team and its major league affiliate. Generally, the parent major league club pays the salaries and benefits of uniformed personnel (players and coaches) and bats and balls, while the minor league club pays for in-season travel and other operational expenses.

Minor league teams often change their affiliation with major league clubs for a variety of reasons. Sometimes Major or Minor League clubs wish to affiliate with a partner that is geographically closer. In recent years, some MLB clubs have attempted to place as many affiliated teams within their blackout area as possible, in order to make scouting and player transfers more convenient and to take advantage of the existing fan base when interest in the parent team builds support for the minor league affiliate and early fan interest in developing minor league players reinforces support for the parent team as "local players" reach the majors.

Sometimes a Minor League club wishes to improve the caliber of players its major league affiliate sends to play there. Sometimes a major league club wishes to improve the facility where it will send its developing players. In even-numbered years, any Major or Minor League club with an expiring PDC may notify Major League Baseball or Minor League Baseball, respectively, of its desire to explore a re-affiliation with a different PDC partner. The Major League Baseball and Minor League Baseball offices then send a list of the corresponding Major and Minor League clubs seeking new affiliations, and there is a limited period of time in September within which clubs may agree upon new PDC. If any are left over after this process, the Major League Baseball and Minor League Baseball offices are empowered to assign Major and Minor League clubs to each other.

The current minor league classification system divides leagues into one of five classes, those being Triple-A (AAA), Double-A (AA), Low-A (Single-A or A), Low-A Short Season, and Rookie. Furthermore, Low-A is further subdivided into Low-A and Low-A-Advanced (often called Low-A and High-A, respectively). Under the rules governing the affiliated minor leagues (specifically Major League Baseball Rule 51); Low-A Short Season is a separate classification from the other leagues bearing the "Low-A" name, despite the similarity in name.