The Arizona Diamondbacks had the highest run differential by a team in 1999, with a differential of 232 runs.

	TEAM	DIFF	SEASON	G	W%	W	L	AB	R	H	2B	3B	HR	RBI	BB	HBP	SO	SB	CS	PA	TB	XBH	SH	SF	IBB	GIDP	AVG	OBP	SLG	OPS
1	Diamondbacks	232	1999	162	.617	100	62	5,658	908	1,566	289	46	216	865	588	48	1,045	137	39	6,415	2,595	551	61	60	52	94	.277	.347	.459	.805
2	Braves	179	1999	162	.636	103	59	5,569	840	1,481	309	23	197	791	608	53	962	148	66	6,351	2,427	529	74	47	62	120	.266	.341	.436	.777
3	Yankees	169	1999	162	.605	98	64	5,568	900	1,568	302	36	193	855	718	55	978	104	57	6,416	2,521	531	22	53	47	137	.282	.366	.453	.819
4	Reds	154	1999	163	.589	96	67	5,649	865	1,536	312	37	209	820	569	45	1,125	164	54	6,377	2,549	558	70	44	37	107	.272	.341	.451	.792
5	Indians	149	1999	162	.599	97	65	5,634	1,009	1,629	309	32	209	960	743	55	1,099	147	50	6,553	2,629	550	54	67	41	136	.289	.373	.467	.840
6	Astros	148	1999	162	.599	97	65	5,485	823	1,463	293	23	168	784	728	52	1,138	166	75	6,402	2,306	484	79	58	57	127	.267	.355	.420	.775
7	Mets	142	1999	163	.595	97	66	5,572	853	1,553	297	14	181	814	717	48	994	150	61	6,454	2,421	492	63	54	53	149	.279	.363	.434	.797
8	Red Sox	118	1999	162	.580	94	68	5,579	836	1,551	334	42	176	808	597	55	928	67	39	6,321	2,497	552	34	56	27	131	.278	.350	.448	.798
9	Rangers	86	1999	162	.586	95	67	5,651	945	1,653	304	29	230	897	611	29	937	111	54	6,388	2,705	563	35	62	41	147	.293	.361	.479	.840
10	Athletics	47	1999	162	.537	87	75	5,519	893	1,430	287	20	235	845	770	71	1,129	70	37	6,440	2,462	542	39	41	32	129	.259	.355	.446	.801
11	Giants	41	1999	162	.531	86	76	5,563	872	1,507	307	18	188	828	696	60	1,028	109	56	6,448	2,414	513	87	42	40	129	.271	.356	.434	.790
12	Orioles	36	1999	162	.481	78	84	5,637	851	1,572	299	21	203	804	615	61	890	107	46	6,409	2,522	523	41	55	34	146	.279	.353	.447	.800
13	Blue Jays	21	1999	162	.519	84	78	5,642	883	1,580	337	14	212	856	578	76	1,077	119	48	6,369	2,581	563	28	45	29	129	.280	.352	.457	.810
14	Dodgers	6	1999	162	.475	77	85	5,567	793	1,480	253	23	187	761	594	52	1,030	167	68	6,338	2,340	463	74	51	34	109	.266	.339	.420	.760
15	Phillies	-5	1999	162	.475	77	85	5,598	841	1,539	302	44	161	797	631	46	1,081	125	35	6,386	2,412	507	70	41	37	127	.275	.351	.431	.782
16	Pirates	-7	1999	161	.484	78	83	5,468	775	1,417	282	40	171	735	573	60	1,197	112	44	6,233	2,292	493	87	45	40	111	.259	.334	.419	.753
17	Cardinals	-29	1999	161	.466	75	86	5,570	809	1,461	274	27	194	763	613	51	1,202	134	48	6,353	2,371	495	75	44	51	110	.262	.338	.426	.764
18	Mariners	-46	1999	162	.488	79	83	5,572	859	1,499	263	21	244	825	610	42	1,095	130	45	6,310	2,536	528	38	48	38	114	.269	.343	.455	.798
19	Royals	-65	1999	161	.398	64	97	5,624	856	1,584	294	52	151	800	535	64	932	127	39	6,325	2,435	497	46	56	25	156	.282	.348	.433	.781
20	Padres	-71	1999	162	.457	74	88	5,394	710	1,360	256	22	153	671	631	35	1,169	174	67	6,136	2,119	431	36	40	31	132	.252	.332	.393	.725
21	Brewers	-71	1999	161	.460	74	87	5,582	815	1,524	299	30	165	777	658	55	1,065	81	33	6,433	2,378	494	87	51	44	110	.273	.353	.426	.779
22	White Sox	-93	1999	162	.466	75	86	5,644	777	1,563	298	37	162	742	499	34	810	110	50	6,262	2,421	497	40	45	22	138	.277	.337	.429	.766
23	Angels	-115	1999	162	.432	70	92	5,494	711	1,404	248	22	158	673	511	43	1,022	71	45	6,131	2,170	428	41	42	24	135	.256	.322	.395	.716
24	Rockies	-122	1999	162	.444	72	90	5,717	906	1,644	305	39	223	863	508	43	863	70	43	6,368	2,696	567	54	46	31	125	.288	.348	.472	.819
25	Tigers	-135	1999	161	.429	69	92	5,481	747	1,433	289	34	212	704	458	82	1,049	108	70	6,095	2,426	535	35	39	19	108	.261	.326	.443	.768