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In 2000, the number of JFL teams was increased to 12, suggesting that the league was on a comeback trail. The new teams were drawn mainly from the top level of local prefectural leagues, such as Ehime FC, Ibaraki FC and Alo's Hokuriku. The inclusion of these teams contributed to the spread of interest in football, to all a parts of Japan. The most important news for the JFL was the fact that Yokohama FC won the league championship for the second consecutive year, and thus gained promotion to the J2 after "rising from the ashes" in 1999. This success was not only good for Yokohama FC; it also brought needed publicity to the JFL.
Considering the long history of the JFL, and its persistence in reforming itself despite repeated "raids" by the J.League, it is perhaps no surprise that the league rebounded quickly to 12 teams following the J2's creation in 1999. Japan's football organisations all were very eager to ensure that the JFL would become a strong third division in Japan's football hierarchy, though it would be another three or four years before its role with respect to the J1 and J2 would be fully clarified.
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| Rank | Team | GP | Win | D | L | GF | GA | G.Dif | Pts |
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| 90 | ET |
| 1 | Yokohama FC | 21 | 18 | 1 | 2 | 0 | 63 | 24 | +39 | 58 | | 2 | Honda Giken | 21 | 14 | 2 | 0 | 5 | 46 | 29 | +17 | 46 | | 3 | Denso | 21 | 11 | 4 | 1 | 5 | 41 | 22 | +19 | 42 | | 4 | Otsuka FC | 21 | 12 | 2 | 0 | 7 | 57 | 36 | +21 | 40 | | 5 | Sony Sendai | 21 | 10 | 2 | 0 | 9 | 50 | 37 | +13 | 34 | | 6 | Jatco TT | 21 | 9 | 0 | 1 | 11 | 42 | 43 | -1 | 28 | | 7 | Kokugikan U. | 21 | 7 | 3 | 1 | 10 | 44 | 46 | -2 | 28 | | 8 | Alo's Hokuriku | 21 | 6 | 2 | 0 | 13 | 26 | 46 | -20 | 22 | | 9 | FC Kyoken | 21 | 3 | 3 | 1 | 14 | 19 | 38 | -19 | 16 | | 10 | Shizuoka Tech. | 21 | 4 | 1 | 2 | 14 | 25 | 45 | -20 | 16 | | 11 | Ibaraki SC | 21 | 2 | 2 | 1 | 16 | 20 | 48 | -28 | 11 | | 12 | Yokogawa FC | 21 | 2 | 0 | 3 | 16 | 21 | 40 | -19 | 9 |
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