Abstract The somatic cell count (SCC) is one of the international standards for monitoring milk quality, and it is a useful indicator of mastitis. The current reference method for determining the SCC in raw milk is direct microscopic analysis, but this method requires well-trained staff to maintain its accuracy and reproducibility. To overcome these inconveniences, we developed a portable system (the C-reader system) that utilizes the capillary flow of a microfluidic chamber by surface modification of the hydrophilicity. The microfluidic technology of disposable microchips allows for low consumption of reagents, and a combination of ready-to-use reagents makes the daily work easier. The repeatability test of the C-reader using 10 composite bovine milk samples satisfied the recommended values for SCC equipment. In addition, an acceptable accuracy level of the natural logarithmic-transformed SCC [ln(SCC/1,000):±0.059 to 0.112] was achieved using composite raw milk samples and various somatic cell standard solutions from the American Eastern Laboratory and the Korean National Veterinary Research and Quarantine Service. After testing 875 composite milk samples, the C-reader showed a high correlation coefficient (R2=0.935 to 0.964) and a low mean difference value in log-transformed SCC (−0.088 to 0.004) compared with 3 automatic commercialized somatic cell counters (Fossomatic 4000, Somacount 150, and Somascope). In conclusion, the C-reader system is a new, easy-to-use automatic on-farm method with acceptable repeatability and accuracy for measuring SCC in large dairies and smaller laboratories.