A sequential injection (SI) system in the capillary format is reported for protein concentration determinations employing sample volumes in the microliter to nanoliter range. By incorporating a programmable syringe pump and computer control over the selection valve and data acquisition system, the invasion plasmid antigen C (IpaC) protein concentration in a purified sample was determined. Results of flow rate, temperature, and injection studies are presented. Replicate measurements of a bovine serum albumin (BSA) standard resulted in a relative standard deviation in peak area of 3.1%. In addition, protein concentrations as low as 5 × 10 −6 M were determined in less than 3 min. This system was subsequently applied to the determination of a real IpaC sample using multiple standard additions. The error in the determination, relative to a spectrophotometric method of determination, was 7.1%. The total sample consumption for the calibration and unknown concentration determination was 60 μl.