Purpose: To compare post-implant dosimetrics between intraoperatively built custom-linked (IBCL) seeds and loose seeds (LS) at 24 hours and 1 month by sector analysis, and to evaluate the effect of IBCL seeds with regard to change in dosimetric parameters, in patients with prostate cancer treated with brachytherapy. Material and methods: Consecutive patients treated for localized prostate cancer who received definitive brachytherapy between March 2013 and October 2017 were retrospectively analyzed. Prostate V 100 (PV 100), prostate D 90 (PD 90), prostate V 150 (PV 150), urethral D 30 (UD 30), urethral V 150 (UV 150), and rectal V 100 (RV 100) were assessed. Results: Thirty-two patients were treated with LS and 32 patients were treated with IBCL seeds. The median follow-up time was 49.9 months in the LS group and 27.1 months in the IBCL group. PV 150 , UV 150 , and UD 30 at 24 hours and UD 30 at 1 month showed significant difference (F-test), and standard deviation (SD) tended to be lower in the IBCL group. Analysis of change in the variables revealed significance for ΔPV 100 and ΔPD 90 (F-test, p = 0.014 and < 0.001, respectively), and ΔPV 150 and ΔUD 30 showed marginal significance (p = 0.084 and 0.097, respectively). PV 150 , UV 150 , and UD 30 at 24 hours and 1 month were significantly lower in the IBCL group, and there was no significant difference in PV 100 , PD 90 , and RV 100 compared with the LS group (t-test). The homogeneity index (HI) was significantly higher in the IBCL group (p < 0.001). Conclusions: In this retrospective single institutional study, there was a decrease in the SD of the dosimetric parameters in the IBCL group, and it was statistically significant in change in the variables between 24 hours and 1 month (F-test). The use of IBCL seeds significantly decreased PV 150 , UV 150 , and UD 30 , and significantly improved HI, without lowering PD 90 or PD 100 .