The third edition of the European Short Course Championships was held in Complexo Desportivo do Jamor in Lisboa, Portugal, from 9 to 11 December 1999.

  *   Host nation (Portugal)

Rank	Nation	Gold	Silver	Bronze	Total
1	Sweden (SWE)	9	7	1	17
2	Germany (GER)	6	12	8	26
3	Ukraine (UKR)	5	1	3	9
4	Great Britain (GBR)	3	3	9	15
5	Netherlands (NED)	3	1	2	6
6	Spain (ESP)	2	2	1	5
7	Croatia (CRO)	2	1	0	3
	Slovakia (SVK)	2	1	0	3
9	Iceland (ISL)	2	0	0	2
10	Denmark (DEN)	1	1	2	4
	Italy (ITA)	1	1	2	4
12	Belgium (BEL)	1	0	1	2
	Russia (RUS)	1	0	1	2
14	France (FRA)	1	0	0	1
15	Hungary (HUN)	0	3	0	3
16	Belarus (BLR)	0	1	1	2
	Portugal (POR)*	0	1	1	2
	Slovenia (SLO)	0	1	1	2
	Switzerland (SUI)	0	1	1	2
20	Turkey (TUR)	0	1	0	1
21	Czech Republic (CZE)	0	0	1	1
	Finland (FIN)	0	0	1	1
	Israel (ISR)	0	0	1	1
Totals (23 entries)		39	38	37	114

Event	Gold		Silver		Bronze
50 m freestyle	Mark Foster  Great Britain	21.71	Pieter van den Hoogenband  Netherlands	21.79	Lorenzo Vismara  Italy	21.83
100 m freestyle	Pieter van den Hoogenband  Netherlands	47.20	Lars Frölander  Sweden	47.86	Karel Novy  Switzerland	48.44
200 m freestyle	Pieter van den Hoogenband  Netherlands	1:44.34	Massimiliano Rosolino  Italy	1:45.22	Stefan Herbst  Germany	1:46.09
400 m freestyle	Massimiliano Rosolino  Italy	3:42.00	Jörg Hoffmann  Germany	3:42.88	James Salter  Great Britain	3:43.48
1500 m freestyle	Igor Chervynskyi  Ukraine	14:42.05	Jörg Hoffmann  Germany	14:45.71	Teo Edo  Spain	14:59.43
50 m backstroke	Miro Žeravica  Croatia	24.70	Tomislav Karlo  Croatia	24.72	Sebastian Halgasch  Germany	24.79
100 m backstroke	Örn Arnarson  Iceland	53.13	Derya Büyükuncu  Turkey	53.17	Volodymyr Nikolaychuk  Ukraine	53.27
200 m backstroke	Örn Arnarson  Iceland	1:54.23	Jirka Letzin  Germany	1:55.19	Adam Ruckwood  Great Britain	1:55.25
50 m breaststroke	Mark Warnecke  Germany	27.10	Oleg Lisogor  Ukraine	27.37	Roman Sloudnov  Russia	27.38
100 m breaststroke	Roman Sloudnov  Russia	58.85	Patrik Isaksson  Sweden	59.32	José Couto  Portugal	59.70
200 m breaststroke	Stéphan Perrot  France	2:07.82	José Couto  Portugal	2:09.98	Adam Whitehead  Great Britain	2:10.98
50 m butterfly	Miloš Milošević  Croatia Lars Frölander  Sweden	23.35	None		Jere Hård  Finland	23.81
100 m butterfly	Lars Frölander  Sweden	51.19	James Hickman  Great Britain	51.43	Denys Sylantyev  Ukraine	52.01
200 m butterfly	James Hickman  Great Britain	1:53.52	Thomas Rupprath  Germany	1:54.43	Denys Sylantyev  Ukraine	1:54.86
100 m individual medley	Jens Kruppa  Germany	53.93	Peter Mankoč  Slovenia	54.27	Marcel Wouda  Netherlands	54.38
200 m individual medley	Marcel Wouda  Netherlands	1:56.46	Jirka Letzin  Germany	1:58.23	Massimiliano Rosolino  Italy	1:58.57
400 m individual medley	Frederik Hviid  Spain	4:08.85	Jirka Letzin  Germany	4:09.85	Michael Halika  Israel	4:12.25
4×50 m freestyle relay	Sweden Claes Andersson Lars Frölander Stefan Nystrand Daniel Carlsson	1:27.12	Germany Mitja Zastrow Alexander Lüderitz Stephan Kunzelmann Kai Hanschmann	1:27.76	Netherlands Dennis Rijnbeek Stefan Aartsen Marcel Wouda Pieter van den Hoogenband	1:27.95
4×50 m medley relay	Sweden Daniel Carlsson Patrik Isaksson Lars Frölander Stefan Nystrand	1:36.00	Germany Sebastian Halgasch Mark Warnecke Thomas Rupprath Alexander Lüderitz	1:36.56	Great Britain Neil Willey Darren Mew James Hickman Mark Foster	1:36.78

Event	Gold		Silver		Bronze
50 m freestyle	Therese Alshammar  Sweden	24.09 WR	Anna-Karin Kammerling  Sweden Sue Rolph  Great Britain	24.90	None
100 m freestyle	Therese Alshammar  Sweden	52.80 WR	Sue Rolph  Great Britain	53.26	Sandra Völker  Germany	53.34
200 m freestyle	Martina Moravcová  Slovakia	1:56.28	Josefin Lillhage  Sweden	1:57.15	Natalya Baranovskaya  Belarus	1:57.33
400 m freestyle	Yana Klochkova  Ukraine	4:05.12	Natalya Baranovskaya  Belarus	4:06.13	Silvia Szalai  Germany	4:06.48
800 m freestyle	Yana Klochkova  Ukraine	8:22.37	Flavia Rigamonti  Switzerland	8:25.82	Jana Henke  Germany	8:28.89
50 m backstroke	Sandra Völker  Germany	27.31	Nina Zhivanevskaya  Spain	28.24	Antje Buschschulte  Germany	28.35
100 m backstroke	Nina Zhivanevskaya  Spain	59.87	Antje Buschschulte  Germany	1:00.08	Sarah Price  Great Britain	1:00.88
200 m backstroke	Antje Buschschulte  Germany	2.08.11	Nina Zhivanevskaya  Spain	2.09.47	Nicole Hetzer  Germany	2.09.62
50 m breaststroke	Zoë Baker  Great Britain	31.40	Ágnes Kovács  Hungary	31.49	Janne Schäfer  Germany	31.95
100 m breaststroke	Brigitte Becue  Belgium	1:08.15	Ágnes Kovács  Hungary	1:08.30	Emma Igelström  Sweden	1:08.74
200 m breaststroke	Anne Poleska  Germany	2:24.78	Ágnes Kovács  Hungary	2:25.41	Brigitte Becue  Belgium	2:26.82
50 m butterfly	Anna-Karin Kammerling  Sweden	25.64 WR	Johanna Sjöberg  Sweden	26.42	Nicola Jackson  Great Britain	27.17
100 m butterfly	Johanna Sjöberg  Sweden	57.73	Mette Jacobsen  Denmark	59.11	Sophia Skou  Denmark	59.80
200 m butterfly	Mette Jacobsen  Denmark	2:06.87	Johanna Sjöberg  Sweden	2:08.62	Sophia Skou  Denmark	2:09.33
100 m individual medley	Martina Moravcová  Slovakia	1:00.78	Annika Mehlhorn  Germany	1:01.82	Nataša Kejžar  Slovenia	1:02.16
200 m individual medley	Yana Klochkova  Ukraine	2:09.08	Martina Moravcová  Slovakia	2:09.25	Sue Rolph  Great Britain	2:11.29
400 m individual medley	Yana Klochkova  Ukraine	4:34.07	Nicole Hetzer  Germany	4:37.47	Hana Černá  Czech Republic	4:37.74
4×50 m freestyle relay	Sweden Johanna Sjöberg Therese Alshammar Anna-Karin Kammerling Malin Svahnström	1:38.45 WBT	Germany Katrin Meissner Simone Osygus Sandra Völker Britta Steffen	1:39.21	Great Britain Alison Sheppard Nicola Jackson Karen Pickering Sue Rolph	1:39.93
4×50 m medley relay	Sweden Therese Alshammar Emma Igelström Johanna Sjöberg Anna-Karin Kammerling	1:49.47 WBT	Germany Sandra Völker Janne Schäfer Marietta Uhle Katrin Meissner	1:49.87	Great Britain Katy Sexton Zoë Baker Nicola Jackson Sue Rolph	1:51.64

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