Between the 2003 and 2006 seasons, the New York Yankees had the most wins by a team, with 394 wins.

Interpreted as:

most regular-season wins by an MLB team 2003 to 2006

	TEAM	W	L	W%	G	AB	R	H	2B	3B	HR	RBI	BB	HBP	SO	SB	CS	PA	TB	XBH	SH	SF	IBB	GIDP	AVG	OBP	SLG	OPS
1	Yankees	394	254	.608	649	22,407	3,590	6,161	1,171	71	911	3,457	2,640	306	4,066	405	128	25,654	10,207	2,153	124	177	178	575	.275	.357	.456	.812
2	Red Sox	374	274	.577	648	22,734	3,640	6,369	1,410	102	851	3,484	2,604	235	4,232	252	100	25,883	10,536	2,363	72	238	190	520	.280	.357	.463	.820
3	Cardinals	373	274	.577	647	22,287	3,317	6,102	1,240	109	764	3,146	2,193	247	3,906	335	147	25,234	9,852	2,113	308	199	262	513	.274	.343	.442	.785
4	Athletics	368	280	.568	648	22,352	3,104	5,848	1,229	81	695	2,968	2,351	216	3,754	187	78	25,202	9,324	2,005	91	192	142	578	.262	.335	.417	.752
5	Braves	366	282	.565	648	22,309	3,328	6,074	1,245	131	819	3,190	2,192	205	4,344	298	121	25,186	10,038	2,195	293	187	201	524	.272	.340	.450	.790
6	Twins	361	287	.557	648	22,444	3,070	6,110	1,172	135	623	2,888	2,000	236	3,859	413	176	25,030	9,421	1,930	161	189	173	587	.272	.336	.420	.755
7	White Sox	358	290	.552	648	22,207	3,265	5,962	1,131	81	898	3,141	1,955	258	4,004	385	195	24,807	9,949	2,110	198	189	112	491	.268	.332	.448	.780
8	Angels	353	295	.545	648	22,395	3,099	6,135	1,135	129	618	2,933	1,859	200	3,542	581	221	24,817	9,382	1,882	180	183	185	499	.274	.333	.419	.752
9	Astros	350	298	.540	649	22,034	3,036	5,731	1,158	125	713	2,881	2,213	287	4,133	349	140	25,053	9,278	1,996	341	178	195	491	.260	.333	.421	.754
10	Phillies	345	303	.532	648	22,415	3,303	5,965	1,204	126	764	3,142	2,561	264	4,574	380	108	25,643	9,713	2,094	229	174	259	465	.266	.346	.433	.779
11	Giants	342	304	.529	646	21,936	3,000	5,785	1,191	140	654	2,846	2,223	214	3,646	225	120	24,883	9,218	1,985	339	171	334	555	.264	.335	.420	.755
12	Dodgers	337	311	.520	648	22,061	2,840	5,704	1,077	134	629	2,715	2,085	252	4,130	368	161	24,805	8,936	1,840	263	144	179	521	.259	.328	.405	.733
13	Marlins	335	313	.517	648	21,980	2,944	5,859	1,182	150	615	2,777	2,023	256	4,113	452	213	24,749	9,186	1,947	317	173	197	509	.267	.333	.418	.751
14	Cubs	322	326	.497	648	22,318	2,932	5,941	1,204	122	767	2,797	1,795	181	4,086	325	147	24,773	9,690	2,093	311	168	159	521	.266	.324	.434	.758
15	Padres	321	327	.495	648	22,182	2,861	5,844	1,128	141	558	2,716	2,295	202	4,064	350	139	25,115	8,928	1,827	233	203	157	519	.263	.335	.402	.738
16	Blue Jays	320	327	.495	647	22,369	3,197	6,089	1,302	133	670	3,046	2,059	313	4,025	232	124	25,015	9,667	2,105	68	206	114	577	.272	.339	.432	.771
17	Indians	319	329	.492	648	22,476	3,217	6,076	1,329	112	745	3,079	2,131	248	4,368	297	175	25,193	9,864	2,186	162	176	141	526	.270	.338	.439	.777
18	Rangers	319	329	.492	648	22,654	3,386	6,097	1,265	122	909	3,257	1,988	224	4,324	254	100	25,121	10,333	2,296	74	181	127	477	.269	.332	.456	.788
19	Mets	317	330	.490	647	21,936	2,882	5,583	1,153	117	684	2,748	2,034	225	4,340	476	129	24,652	9,022	1,954	293	164	208	482	.255	.322	.411	.733
20	Mariners	303	345	.468	648	22,460	2,948	6,001	1,121	129	577	2,777	1,948	218	4,007	426	163	24,951	9,111	1,827	156	169	182	493	.267	.329	.406	.735
21	Nationals	302	346	.466	648	21,832	2,731	5,569	1,203	106	576	2,597	2,103	238	4,161	377	184	24,679	8,712	1,885	339	167	230	506	.255	.325	.399	.724
22	Reds	298	350	.460	649	22,107	3,013	5,601	1,152	76	815	2,884	2,348	281	5,156	353	115	25,100	9,350	2,043	230	134	166	465	.253	.331	.423	.754
23	Orioles	293	355	.452	649	22,562	3,082	6,178	1,180	89	674	2,925	1,880	238	3,631	394	146	25,042	9,558	1,943	177	185	132	539	.274	.334	.424	.757
24	Brewers	291	356	.450	647	21,912	2,804	5,594	1,189	95	686	2,670	2,120	294	4,928	387	150	24,739	9,031	1,970	242	171	193	548	.255	.327	.412	.739
25	Diamondbacks	288	360	.444	648	22,309	2,801	5,793	1,220	150	638	2,691	2,082	202	4,087	272	126	25,031	9,227	2,008	251	187	199	531	.260	.326	.414	.740