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This experiment investigated changes in body composition throughout lactation in dairy goats using non-invasive methods of body composition estimation including dual-energy X-ray absorptiometry (DEXA), body weight (BW), body condition score (BCS), and body mass index (BMI) in lactating Saanen dairy goats (20 high producers and 20 low producers). Body composition was measured on four occasions, early lactation (EL, 23 ± 6 DIM), mid lactation (ML, 107 ± 6 DIM), late lactation (LL, 206 ± 6 DIM), and 2 weeks post drying-off. The DEXA scans provide estimates of fat and lean tissue mass, and were evaluated by region (whole body, lower body, and sternal area). Data were analyzed using restricted maximum likelihood (REML) with stage of lactation and production group as fixed effects and goat as the random effect to account for repeated measurements within animals. Correlations among body composition measures were assessed using Pearson's coefficients. Differences in body composition were driven primarily by stage of lactation rather than by production group. Milk yield was greatest in high producers during EL only (3.2 vs. 2.5 L/d; P < 0.05), but no differences were observed in energy corrected milk. The BW and BCS increased throughout lactation, peaking during the dry period. Changes in DEXA-derived fat and lean tissue mass were observed, with the largest change observed in sternal fat from EL to ML (-17%; P < 0.001). The BMI had stronger correlations with DEXA-derived body composition measures compared to BCS (r = 0.78 vs. 0.58; P < 0.001). Changes in composition were associated with changes in lactation stage rather than production level. While BW and BCS increased, overall, DEXA-derived fat mass decreased throughout lactation by 14% and increased by 10% from LL to the dry period (P < 0.001). To our knowledge, this is the first experiment to apply DEXA to measure body composition throughout lactation in goats. Findings suggest BMI may be a more reliable indicator of DEXA-derived body composition compared to BCS.