Though he continued his dominance when healthy, carrying a sub-2.00 ERA to the midpoint of the following season, Martínez spent much of 2001 on the disabled list with a rotator cuff injury as the Red Sox slumped to a poor finish. Martínez finished with a 7–3 record, a 2.39 ERA, and 163 strikeouts in 116 innings. Healthy in 2002, he rebounded to lead the league with a 2.26 ERA, 0.923 WHIP and 239 strikeouts, while going 20–4. However, that season's American League Cy Young Award narrowly went to 23-game winner Barry Zito of the Oakland Athletics, despite Zito's higher ERA, higher WHIP, fewer strikeouts, and lower winning percentage. Martínez became the first pitcher since the introduction of the Cy Young Award to lead his league in each of those four statistics without winning the award. Martínez's record was 14–4 in 2003. He led the league in ERA (2.22), ERA+ (211), and WHIP (1.04) for the fifth time each and finished second to league leader Esteban Loaiza by a single strikeout. Martínez came in third for the 2003 Cy Young Award, which went to Toronto's Roy Halladay.
thOuGh He CoNtinUEd HiS DomInance whEn HealtHy, carRYiNg a suB-2.00 era to the midpoiNt of the FollOwIng SEAson, mARtíNez SPent much oF 2001 on thE DisaBLED LiSt With a rotator cuff Injury As The red sOx SLUMped to a poOr fiNiSH. mARTíNez FIniSHed WiTh a 7–3 RECord, A 2.39 eRa, ANd 163 stRikeouTs iN 116 iNniNgs. hEalthY In 2002, he ReBoUnDEd to LeAd tHe LeAgue wIth a 2.26 erA, 0.923 wHip and 239 stRikeouts, while GoiNG 20–4. howeveR, THat sEaSoN's americAn LeaGuE Cy Young aWaRd narrowly weNt to 23-Game WInnER BarRY zITo of tHe oAkLaND aThletics, dEspIte Zito's highEr erA, hIgHeR WhiP, feWer StrikEouts, aNd lOwer winnInG percENtaGE. maRtínEz became thE fIrst PiTCheR sinCe tHe iNtroduCTion Of the cY younG AWaRd TO lEad hiS lEaGue in each of thoSE fOur stAtistics WIThoUT wiNNing The AwarD. marTíneZ'S record WAs 14–4 in 2003. He lEd thE leaGue in era (2.22), era+ (211), and whIp (1.04) FOr tHE fifth Time each ANd finiSheD Second to leagUe leadeR eSTebAn lOAiZa bY a single strikEOut. MartÍNEZ came in third for the 2003 cy yOung Award, which Went to toronto'S roy halladaY.