CDT (Carbohydrate Deficient Transferrin) is considered as the most efficient biomarker of alcohol abuse available for routine use. Among the various methods developed for its measurement, capillary zone electrophoresis (CZE) on the multicapillary analyzer Capillarys2 provides high quality results at high throughput. However, the non CDT specific measurement of protein absorbance at 200 nm may bring abnormal profiles in samples from patients with high polyclonal immunoglobulin level or monoclonal component. We evaluated the automated immunosubtraction procedure developed by the manufacturer in 48 samples with abnormal electrophoretic profiles that potentially could interfere with CZE measurement of CDT. Elimination of the serum immunoglobulins raised the number of interpretable profiles from 19 (40%) to 37 (77%). The immunosubtraction procedure failed in samples with a monoclonal component present at a concentration > 60 g/L and in some samples harbouring a partially degraded C3 fraction. Six samples identified as genetic BC transferrin variants were also included in the study and submitted to an automated transferrin subtraction procedure to ascertain whether the additional peak were actually transferrin glycoforms. After treatment, two samples were classified as homozygote C for transferrin due to the persistence of one of the supposed transferrin peak. In conclusion, immunoglobulin and transferrin subtraction allow a better CDT measurement in most samples with interfering monoclonal components and avoid misclassification of suspected transferrin BC or CD variants.