CSL and IDEXX test kits for antibody to Mycobacterium paratuberculosis were compared for their relative reproducibility and correlation of test results with faecal culture analysis. A panel of 10 standard samples was tested in each plate to compare between-run variation of the two kits. Also, each lab chose 108 unique sera, with 1/3 of them tested in each run to compare between-duplicate variation and agreement with faecal status for the two test kits. The median coefficient of variation (CV) for duplicates of the 108 samples run in each lab on the CSL kit was 4.3%, 3.8%, 9.9% and 20.0% for the 4 labs, respectively (mean = 7.1%). The comparable data for the IDEXX test kit was 3.1%, 2.6%, 4.9% and 3.2% (mean = 3.5%). The average CV for three runs of the 10 standard samples run in the CSL assay was 2.0%, 3.8% and 9.8% for three of the labs (average of 5.2%), while the comparable data on the IDEXX assay was 27.6%, 4.1%, and 21.8% (average of 17.8%). (The fourth lab inadvertently tested all samples in one 3-plate run using only 1 set of standards for the CSL kit so CV's for standards could not be calculated for comparison with the IDEXX kit data). Calculation of ratios to normalise the IDEXX results, as per kit instructions, increased the average for the median CVs of the three labs to about 25.7% (outliers eliminated to reduce bias). Antibody test results were discrepant between the CSL and IDEXX assays for 90 of the 481 samples (20.7%). Faecal culture status agreed with both assays for 62.1%-12.4% (SD) of the animals tested. Faecal culture status agreed with antibody test results slightly more often for the CSL assay (74.0%-7.0%) than for the IDEXX assay (71.0%-11.9%). The major difference between kits was the between-run variation in the IDEXX kit using normalised data (ratios as specified in kit instructions); it was about 3.4 times greater than the CSL non-normalised ODs - an unexpected result. Such differences indicate the need for a more in-depth study to isolate and rectify the source(s) of error that may affect serological classification of animal infection status.