All three of the leagues folded within a few years or operated off and on during the late 1800s. Dozens of other Minor Leagues quickly formed in the 1880s and the 1890s, but many of them were also short lived. Early minor leagues were often state organizations, such as the Connecticut, Kansas, Ohio State, and Texas Leagues. Regional leagues, such as the Central Atlantic League, the Tri-State League (in the Midwest), and the Northwestern League with teams from the state of Washington and British Columbia, also formed. A Canadian league, established in 1899, included teams primarily from province of Ontario.

Changes In Structure: In the late 1800s and early 1900s, Minor Leagues were independent of the Majors, and competition among Major League clubs to obtain players from the Minor teams was intense. A club with the National League or the American League (which declared Major League status in 1901) would shamelessly raid the other Minor League teams, and would sometimes sign up players already under contract without compensating the Minor League team. The Major League teams would go into bidding wars to purchase a Minor League player's contract. As a result, the Minor League formed the National Association of Professional Baseball Leagues (NAPBL), to protect themselves.

The NAPBL established rules for player contracts and allows Major League teams to draft no more than eight Minor League players a year. It also set up a classification system, with A as the highest and D as the lowest. The classification has changed numerous times.

However, Major league teams didn't have direct affiliations with Minor League teams until 1920, when Branch Rickey developed what is known as the farm system. The farm system is the system in which Major League teams set up their own Minor League teams to train players for their team.

Outside the System: Until the 1860s, baseball was mainly a white male's sport. However, in the 1870s, black men were allowed to join some Minor League teams. However, in the late 1880s, blacks were no longer allowed on the teams. Then in 1945 blacks were once again allowed to join the teams.

In 1941, when the U.S. entered W.W.II, the Majors and the Minors started the All-American Girls Professional Baseball League (AAGPBL). Up until then, girls weren't allowed to play professional baseball.

Success Stories: the Minor League has also had some very successful stories, such as the Cincinnati Streak and the home run king, Joe Bouman. Joe Bouman hit 72 home runs in 1954.
 The Salt Lake City Trappers won 27 consecutive games in 1987. John Groennert pitched the winning streak. It was called the Cincinnati Streak because the Salt Lake City Trappers are a Minor League team affiliated with the Cincinnati Reds.