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The 1999–2000 EHF Women's Champions League was the seventh edition of the modern era of the premier competition for European national champions women's handball clubs, running from 1 October 1999 to 27 May 2000. Hypo Niederösterreich defeated Macedonia's Gjorce Petrov in the final to win its eighth title,^[1] with Budućnost Podgorica (which defeated defending champion Dunaferr NK in the quarter-finals) and Dynamo Volgograd also reaching the semifinals.^[2]

Qualifying round

Team #1	Agg.	Team #2	1st	2nd
Politechnik Minsk	45–70	HC Leipzig	29–32	16–38
Westfriesland	35–74	Metz Handball	16–33	19–41
Gjorce Petrov	73–24	HBC Bascharage	41–11	32–13
Baekkelagets	54–37	Slavia Prague	25–19	29–18
HC Motor Zaporizhzhia	76–19	Kefalovrysos Kythreas	39–11	37–8
SPR Lublin	73–43	Sävsjö HK	37–21	36–22
Hypo NÖ	90–45	De Gasperi	42–16	48–29
Anadolu	32–56	Krim Ljubljana	17–26	15–33
Fémina Visé	31–80	Viborg HK	19–39	12–41
Martve Tbilisi	20–97	Budućnost Podgorica	10–52	10–45
Anagennisi Artas	62–53	Madeira	34–24	28–29
Dynamo Volgograd	48–45	Oltchim Ramnicu Valcea	26–26	22–19
TSV St. Otmar St. Gallen	31–85	Ferencvárosi TC	17–39	14–46
Podravka Koprivnica	37–36	Banska Bystrica	22–18	15–18

Team	Pld	W	D	L	GF	GA	GDorg	Pts
Gjorce Petrov	6	3	1	2	141	146	−5	7
Ferencvárosi TC	6	3	0	3	156	149	+7	6
Metz Handball	6	3	0	3	130	121	+9	6
Viborg HK	6	2	1	3	138	149	−11	5

Team	Pld	W	D	L	GF	GA	GDorg	Pts
Hypo NÖ	6	5	1	0	177	143	+34	7
Baekkelagets	6	3	0	3	151	148	+3	6
Krim Ljubljana	6	2	1	3	153	146	+7	5
HC Motor Zaporizhzhia	6	1	0	5	119	163	−44	2

Team	Pld	W	D	L	GF	GA	GDorg	Pts
Budućnost Podgorica	6	4	0	2	172	159	+13	8
Dynamo Volgograd	6	4	0	2	164	149	+156	8
HC Leipzig	6	3	1	2	162	15	+6	7
CBF Elda	6	0	1	5	143	176	−33	1

Team	Pld	W	L	GF	GA	GDorg	Pts
SPR Lublin	6	5	1	172	148	+24	10
Dunaferr NK	6	4	2	177	138	+39	8
Podravka Koprivnica	6	3	3	144	144	0	6
Anagennisi Artas	6	0	6	134	197	−63	0

Team #1	Agg.	Team #2	1st	2nd
Dunaferr NK	58–60	Budućnost Podgorica	33–33	25–27
Ferencvárosi TC	48–52	Hypo NÖ	27–23	21–29
Baekkelagets	41–57	Gjorce Petrov	23–27	18–30
Dynamo Volgograd	56–49	SPR Lublin	28–21	28–28

Team #1	Agg.	Team #2	1st	2nd
Budućnost Podgorica	55–57	Hypo NÖ	28–28	27–29
Gjorce Petrov	45–44	Dynamo Volgograd	23–18	22–26

Team #1	Agg.	Team #2	1st	2nd
Hypo NÖ	52–45	Gjorce Petrov	32–23	20–22