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There are more than 2000 Universities and Colleges in the United States with an intercollegiate Baseball Program. However, not all programs are created equal. The programs attract a different calibre of athlete and are thus organized according to calibre.
The National Collegiate Athletic Association (NCAA) is the governing body of the first 3 divisions for 4-year schools. They organize teams into divisions that are simply labelled as Division I, II and III. Each Division has different level of calibre and resources available. Division I schools generally have larger student bodies, larger budgets and more athletic scholarships. It is easier to be drafted from a Division I school due to exposure and prestige.
Division II has less athletic scholarships available and Division III generally has no athletic scholarships. For baseball, the Southern conferences might be of similar (or higher) calibre to the lower Division I calibres, or at the least, will have student athletes who are draft worthy. It is much harder to be drafted out of Division III schools though it does occur on a yearly basis.
The National Association of Intercollegiate Athletics (NAIA) is a smaller association of schools as compared to the NCAA. NAIA is comparable to school sizes for NCAA Division II and III. The NAIA has fewer schools and also has fewer recruiting restrictions. It has fewer restrictions between player and coaches.
The NJCAA,CCCAA and NWAC are 2-year Junior College associations that are for athletes who wants to attend Junior College instead of 4-year Schools.
Players who attend 4-year schools are only available to be drafted after their Junior Year or are at least 21 years old. Players can be drafted out of Junior College at any time. Players may choose to attend Junior Colleges to get to the Professional ranks sooner or because they are academically not able to attend a 4-year University. There are many Junior College programs that are of high calibre and many programs produce many multiple Pro players and Major Leaguers.
In general, the lower the College class (Fr,So,Jr,Sr), the more leverage the player has for negotiating signing bonus during the amateur entry draft. Seniors, since they don't have any more eligibility remaining have the lowest leverage for signing bonus. Underclassmen can negotiate from a position of strength/leverage since they can return to school for their next college year, and sometimes do.