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This study aimed to identify laboratory factors predicting leprosy relapse (LR) after multi-drug therapy (MDT). A case-control study included 80 patients treated with MDT at a national reference center over 12 years. The Relapse Group had 40 patients who relapsed after an average of 89.2 months post-MDT, while the Control Group had 40 patients who remained asymptomatic for an average of 113.1 months. Significant predictors of LR included neural/perineural lymphocytic infiltrate (OR = 4.67; p = 0.0076) and foamy granulomas (OR = 15.55; p = 0.0005), increasing odds by 4.7 and 15.6 times, respectively. The Relapse Group had a mean histological bacillary index (hBI) of 3.23+ compared to 1.8 in the Control Group (p = 0.004). An hBI ≥3+ had 72% sensitivity and 65% specificity for detecting LR (AUC = 0.72; p = 0.0002). Elevated anti-phenolic glycolipid I (anti-PGL-I) IgM antibody levels (ELISA index, EI ≥1) were also associated with LR (OR = 4.67; p = 0.0031). An EI ≥3.6 had 71% sensitivity and 62% specificity (AUC = 0.70; p = 0.0012). Multivariate analysis indicated that neural/perineural infiltrate, foamy granulomas, hBI ≥ 1+, and EI ≥ 1 significantly predicted LR, with up to 94.32% probability. Conclusively, these factors can identify individuals at high probability of LR after MDT., (© 2024 Scandinavian Societies for Pathology, Medical Microbiology and Immunology.)