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The 1999–2000 Slovenian PrvaLiga season started on 1 August 1999 and ended on 20 May 2000. Each team played a total of 33 matches.

League table

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification or relegation
1	Maribor (C)	33	25	6	2	90	30	+60	81	Qualification to Champions League second qualifying round
2	Gorica	33	19	5	9	55	34	+21	62	Qualification to UEFA Cup qualifying round
3	Rudar Velenje	33	17	7	9	49	35	+14	58
4	Korotan Prevalje	33	15	7	11	58	43	+15	52
5	Primorje	33	13	11	9	56	49	+7	50	Qualification to Intertoto Cup first round
6	Celje	33	11	14	8	53	45	+8	47
7	Olimpija	33	14	4	15	64	58	+6	46	Qualification to UEFA Cup qualifying round^[a]
8	Dravograd	33	11	10	12	44	54	−10	43
9	Domžale	33	11	8	14	50	51	−1	41
10	Mura	33	10	6	17	47	53	−6	36
11	Pohorje (R)	33	4	6	23	26	73	−47	18	Relegation to Slovenian Second League
12	Beltinci (R)	33	3	6	24	21	88	−67	15	Relegation to Slovenian Second League

Source: PrvaLiga (in Slovene)
(C) Champions; (R) Relegated
Notes:

Home \ Away	BEL	CEL	DOM	DRG	GOR	KPR	MAR	MUR	OLI	POH	PRI	RUD
Beltinci		0–0	1–1	1–1	0–0	1–3	0–2	0–3	0–5	1–0	0–5	1–2
Celje	2–0		3–0	0–0	3–3	2–1	1–2	3–2	3–0	1–1	3–1	0–0
Domžale	4–1	5–0		1–1	0–2	1–1	1–4	1–0	2–0	2–1	3–1	0–3
Dravograd	2–0	1–1	2–4		2–4	0–2	1–3	2–1	0–4	2–1	0–0	3–1
Gorica	2–0	1–0	2–0	1–1		2–0	2–1	2–1	2–1	5–0	5–0	0–1
Korotan Prevalje	2–1	1–1	2–2	1–2	0–1		2–4	1–1	3–2	4–0	3–1	1–0
Maribor	5–1	2–1	3–2	2–0	4–0	0–0		3–1	0–0	5–0	2–2	4–1
Mura	1–0	1–3	3–1	2–2	2–0	0–2	2–2		3–0	2–0	1–1	0–3
Olimpija	5–0	3–0	2–0	4–2	4–0	1–5	2–4	2–1		3–1	1–3	1–2
Pohorje	2–1	0–0	1–2	1–3	0–0	3–5	2–1	0–1	0–3		0–0	1–3
Primorje	2–2	2–2	5–1	1–0	1–0	2–2	1–3	1–0	6–0	1–0		2–1
Rudar Velenje	1–0	1–1	1–0	2–0	3–0	2–2	2–2	1–2	0–1	1–0	2–1

Source: PrvaLiga (in Slovene)
Legend: Blue = home team win; Yellow = draw; Red = away team win.

Home \ Away	BEL	CEL	DOM	DRG	GOR	KPR	MAR	MUR	OLI	POH	PRI	RUD
Beltinci			0–4		0–3		0–6			2–3	2–0
Celje	7–0		0–0	2–2				2–1		5–1
Domžale						3–2		0–0	1–2	6–1		0–0
Dravograd	2–0		2–1		1–1		0–3				2–4
Gorica		4–0	2–0			2–1	1–3		3–0	1–0
Korotan Prevalje	1–2	2–1		1–2				3–0			0–1	2–0
Maribor		4–0	1–0			3–0			2–0	3–1		2–1
Mura	6–0			2–3	1–2		1–3				2–1
Olimpija	3–3	2–2		0–1		0–2		5–1				2–2
Pohorje				1–0		0–1		2–2	1–4			2–3
Primorje		2–2	2–2		2–1		2–2		3–2	0–0
Rudar Velenje	2–0	0–2		1–1	2–1			2–1			3–0

Source: PrvaLiga (in Slovene)
Legend: Blue = home team win; Yellow = draw; Red = away team win.

Rank	Player	Club	Goals
1	Kliton Bozgo	Maribor	24
2	Oskar Drobne	Domžale/Gorica	23
3	Uroš Barut	Primorje	17
4	Marko Kmetec	Olimpija	16
5	Aljoša Sivko	Dravograd	14
6	Anton Žlogar	Gorica	13
7	Andrej Goršek	Celje	12
8	Dejan Djuranović	Maribor	11
	Vanja Starčević	Primorje
	Aleksander Radosavljević	Celje