Dye dispersion studies are reported to characterize zone variance in a capillary flow injection system. Variance sources are compared with similar sources in a conventional flow injection system. The inside diameters of the reactors in the capillary and conventional systems were 64 μm and 0.5 mm, respectively. In both systems, reactor length, detector flow cell volume, and injection volume are the major contributors to the total zone variance. The individual contributions of each variance source were determined. Results show that, in a single-line capillary system, the majority of the peak variance is due to extracolumn effects. However, in the conventional system, the reactor was found to be the major contributor to the overall zone variance. Implications of these findings to the development of improved capillary flow injection systems are discussed.