In Japan, the dose of the new recombinant antithrombin III concentrate (rAT-gamma) is titrated according to patient body weight (BW), while conventional plasma-derived antithrombin concentrates (AT) are administered as a fixed dose. Therefore, it is anticipated that rAT-gamma could produce better treatment effects than AT. The aim of this study was to compare the organ protective effects of doses of rAT-gamma and AT administered in clinical practice for septic disseminated intravascular coagulation (DIC) and multiple organ failure. This study was performed at a single university hospital in Japan. A total of 49 patients with antithrombin deficiency secondary to septic DIC who were administered either rAT-gamma (n = 26) or AT (n = 23) were retrospectively analyzed to assess the dose of supplemental antithrombin concentrates, plasma antithrombin activity, Japanese Association for Acute Medicine (JAAM)-DIC score, and modified Sequential Organ Failure Assessment (SOFA) score on days 0, 3 and 6. The AT-equivalent dose per kg BW of rAT-gamma (equal to the initial rAT-gamma dose per kg BW divided by 1.2) was significantly higher than the dose per kg BW of AT (AT 23.4 ± 5.1 vs. rAT 28.9 ± 3.9 IU/kg/day; P < 0.001). Consequently, serial increases in plasma antithrombin levels occurred more rapidly in the rAT-gamma group (P = 0.036). JAAM DIC and modified SOFA scores revealed significantly greater improvement in the rAT versus the AT group (JAAM DIC score: P = 0.042, mSOFA score: P = 0.005). The results of this study suggest that AT supplementation adjusted for patient BW might further improve septic DIC and multiple organ failure.