Abstract Background: Analytical evaluations of an available system for capillary zone electrophoresis (CZE) of serum protein have been reported. However, data concerning long-term precision and stability of the system, operated under routine conditions, are lacking. We report data from an internal quality control (QC) scheme, obtained over a 1-year period. Methods: Measurements were done with a pair of instruments (Beckman Paragon CZE 2000 system), each equipped with seven capillaries. After preliminary (1 month) assessment of possible inter-capillary and inter-instrument variations, the QC material (a home prepared serum pool stored in the frozen state) was assayed daily over a 1-year period. Results: Maximum inter-capillary and inter-instrument differences were 3.1% and 2.4%. No significant trend was observed for daily values (205 measurements over 1 year); in the same period overall imprecision values (CV) were in the interval 1.2% (albumin) to 3.2–6.1% (globulin zones). Mean monthly imprecision (CV) values were in the interval 1.1% (albumin) to 5.2% (globulin zones). There was no significant trend of monthly means with time. The observed imprecision values were within the biological variation-derived goals for imprecision. Conclusions: It is concluded that the assessed analytical instruments, operated in routine conditions, show long-term stability and imprecision consistent with the clinical use of the results produced.