The purpose of this work was to develop a procedure based on protein analysis by free zone capillary electrophoresis (FZCE) that can be used in the determination of smoked paprika "Pimentón de La Vera" adulteration with paprika elaborated from varieties of pepper foreign to the "La Vera" region, in central western Spain. Two autochthonous varieties of pepper, Jaranda and Bola, and the variety Papri Queen, foreign to the "La Vera" region, were used in the study. Several aqueous solutions for solubilization of the methanol-soluble proteins were tested, and the FZCE conditions of capillary dimensions, FZCE buffer concentrations, and detection wavelengths were optimized. On the basis of the results, 30% (v/v) acetonitrile was adopted as the suspending solution for routine analysis, and the optimal FZCE parameters were 75 microm inner diameter and 57 cm total length capillaries, 8.75 mM phosphate/20.6 mM tetraborate as run buffer, and 256 nm as detection wavelength. This method was found to give excellent repeatability of the corrected migration time (CMT) with coefficients of variation (RSD %; n = 5) of <1% for most of the proteinaceous compounds analyzed and showed greater effectiveness in discriminating paprika varieties than the SDS-PAGE technique. Four peaks found in the FZCE electropherograms were investigated as a basis for detecting and estimating the adulteration of smoked paprika with paprika elaborated from the Papri Queen variety. The adulteration detection limits varied from 5 to 40% of the Papri Queen variety within a satisfactory working range of mixture (5-80%) sufficiently large to cover the adulteration levels of interest. The use of peak 6 as a marker for determining adulteration gave the best results, with an adulteration detection limit of 5-10% (w/w).