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The 1999–2000 EHF Women's Cup Winners' Cup was the 24th edition of EHF's competition for women's handball national cup champions. It ran from October 1, 1999, to May 28, 2000.

1997 Champions League champion Mar Valencia became the first Spanish team to win the Cup Winners' Cup, defeating 1988 and 1989 champion Kuban Krasnodar in the final.^[1]

Results

Preliminary round October 1–10, 1999				Round of 16 October 30 – November 7, 1999				Quarterfinals March 18–26, 2000				Semifinals April 22–30, 2000				Final May 20–28, 2000

Iskra Partizánske	22	22	44
Kuban Krasnodar	23	26	49	Kuban Krasnodar	35	34	69
RK Skopje	13	15	28	LC Brühl	24	18	42
LC Brühl	28	25	53					Kuban Krasnodar	29	20	49
								Nordstrand IF	18	16	34
				Nordstrand IF	35	30	65
UHC Stockerau	38	38	76	UHC Stockerau	19	23	42
Kolkheti Poti	14	18	32									Kuban Krasnodar	26	20	46
												Spartak Kyiv	15	30	45
				Larvik HK	36	14	50
Üsküdar Belediyesi	16	15	31	Spartak Kyiv	24	28	52
Spartak Kyiv	45	38	83					Spartak Kyiv	31	26	57
Maccabi Holon	21	13	34					TV Lützellinden	30	29	59
TV Lützellinden	31	44	75	TV Lützellinden	37	39	76
Sporting Neerpelt	36	31	67	Sporting Neerpelt	15	10	25
AC Latsia	15	24	39													Kuban Krasnodar	24	30	54
Lokomotiv Plovdiv	22	25	47													Mar Valencia	31	31	62
Oţelul Galaţi	26	24	50	Oţelul Galaţi	31	27	58
OFN Ionias	21	24	45	OFN Ionias	20	24	44
SK Ulbroka	17	20	37					Oţelul Galaţi	18	22	40
Ikast Bording	27	23	50					Ikast Bording	20	23	43
Napredak Kruševac	22	24	46	Ikast Bording	24	28	52
Olimpija Ljubljana	28	24	52	Olimpija Ljubljana	23	20	43
Cercle Nîmes	15	22	37									Ikast Bording	28	21	49
SV Nieuwegein												Mar Valencia	25	31	56
Kras Zagreb			w/o	Kras Zagreb	28	27	55
Porto Salvo	26	17	43	Start Elblag	29	24	53
Start Elblag	34	40	74					Kras Zagreb	25	25	50
HC Rimini								Mar Valencia	29	32	61
Mar Valencia			w/o	Mar Valencia	29	23	52
Győri Graboplast	48	33	81	Győri ETO	21	27	48
Željezničar Sarajevo	12	13	25