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The aim of this study was to assess important management factors for calves. A) The effects of transdermal flunixin meglumine in combination with local anesthesia during disbudding on 1) plasma cortisol and 2) behavioral changes were evaluated. B) Various analytical methods (RID, ELISA) and on-site measurement methods (digital Brix refractometer, colostrometer, outflow funnel, semi-quantitative immunochromatography) were examined to determine colostrum quality. Additionally, the timing of disbudding was utilized to perform cortisol measurements in different media. Group allocation: 1) Control group (CON, n = 27), 2) 1-Flunixin group (1-FLU, n = 26) with a single administration of transdermal flunixin meglumine during disbudding, and 3) 2-Flunixin group (2-FLU, n = 24) with two administrations of transdermal flunixin meglumine (during disbudding and a second dose 6 hours later). Sham disbudding was performed one week before disbudding using a cold cautery iron. During disbudding, the average plasma cortisol concentration was 5.16 + 2.8 ng/mL (range: 0.2–26.4 ng/mL). Plasma cortisol concentration was influenced by treatment (P < 0.01) and sampling time (P < 0.01). Compared to CON, single treatment (1-FLU) showed a significant effect (P < 0.01; -1.29 ng/mL; 95% CI -2.15 to -0.44), as did the second dose (2-FLU; P < 0.01; -1.29 ng/mL; 95% CI: -2.14 to -0.43). The two groups did not differ significantly from each other (P = 0.99; 0.01 ng/mL; 95% CI: -0.84 to 0.84). Treatment influenced total lying time and lying duration per lying period during sham disbudding (P = 0.01) but had no effect during disbudding (P = 0.31). Additionally, measurements of cortisol in different media (plasma, saliva, feces) were conducted. Cortisol and metabolites were compared. Saliva and fecal samples were collected concurrently with blood samples. The correlation between plasma cortisol and saliva in dairy calves was good (r = 0.73; P < 0.01). The correlation between plasma cortisol and FGM concentration was weak (6 hours: r = 0.24). For colostrum assessment, radial immunodiffusion (RID) was considered the reference method. Colostrum was defined as high-quality if the IgG content of RID measurement was >50 mg IgG/mL. The average IgG concentration (±SD) was 101.3 ± 45.9 mg/mL. The correlation between RID was: r = 0.78 (ELISA), r = 0.79 (digital Brix refractometer), r = 0.58 (colostrometer: specific gravity), r = 0.61 (colostrometer: temperature-corrected), r = 0.26 (outflow funnel), and r = 0.43 (lateral flow assay). The optimal threshold for identifying high-quality colostrum with ELISA was 50.8 mg/mL, with a sensitivity of 91.3%, specificity of 92.3%, and an AUC of 0.94. The sensitivity of on-site tests varied from 95.7% (Brix refractometer) to 60.9% (lateral flow assay). In conclusion, this study shows that 1) transdermal flunixin meglumine can decrease plasma cortisol concentration after disbudding, but 2) has no effect on average daily weight gain and total lying time. 3) ELISA is accurate and 4) the digital Brix refractometer and colostrometer were suitable for assessing colostrum quality.