The Chicago Cubs had the lowest run differential by a team in 1999, with a differential of -173 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	Cubs	-173	1999	162	.414	67	95	5,482	747	1,411	255	35	189	717	571	39	1,170	60	44	6,201	2,303	479	65	44	38	120	.257	.329	.420	.749
2	Marlins	-161	1999	162	.395	64	98	5,578	691	1,465	266	44	128	655	479	59	1,145	92	46	6,216	2,203	438	44	56	30	119	.263	.325	.395	.719
3	Twins	-159	1999	161	.394	63	97	5,495	686	1,450	285	30	105	643	500	49	978	118	60	6,124	2,110	420	24	56	28	151	.264	.328	.384	.712
4	Devil Rays	-141	1999	162	.426	69	93	5,586	772	1,531	272	29	145	728	544	64	1,042	73	49	6,272	2,296	446	30	48	24	157	.274	.343	.411	.754
5	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
6	Expos	-135	1999	162	.420	68	94	5,559	718	1,473	320	47	163	680	438	53	939	70	51	6,149	2,376	530	71	28	39	138	.265	.323	.427	.751
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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