Since the advent of commercial instruments in 1989, capillary electrophoresis (CE) has advanced considerably, with improvement in reproducibility and accuracy in many application fields. CE is predominantly used in research on disease prevention and control, and hygienic chemical inspection. The applications of CE range from assessment of inorganic anions and cations in drinking water to that of biological macromolecules, such as nucleic acids, in pathogenic microorganisms. Since the analytical capacity of CE ranges from inorganic ions to cell, it has become an indispensable technique in this field, particularly in public health emergency and epidemic management. Universal non-targeted analyses to detect possible pathogens, and the capability of rapid and accurate testing of large numbers of specimens are required. In the analyses of polymerase chain reaction (PCR) products, nucleic acid sequencing, mutation detection and genotyping, food-borne disease pathogens, and vaccine analyses, CE methods characterized by high through-put and sensitivity are necessary. In the public health sector, CE is essential in the analyses of food (including emergency analyses for food poisoning), cosmetics, and disinfectants. Satisfactory results of the FAPAS (Food Analysis Performance Assessment Scheme) and domestic proficiency tests indicated the accuracy of CE in quantitative analyses. Application of CE in disease prevention and control is challenged by a number of new molecular biological methods, as optimizing CE methods may not be feasible, and results are difficult to interpret. CE methods, including transformation of peaks to identification of pathogens, can be an arduous task. Thus, end-users prefer using commercialized CE systems and reagents in their routine work. Alternatively, CE methods for analysis of small molecules in product analyses, such as food safety, cosmetics and disinfectant testing, is commonly performed. A plethora of studies published within the decade, indicate that CE is still an active research area in hygienic chemical inspection. To a large extent, CE has not been used for routine analysis in the centers for disease control and prevention, accredited laboratories in China, nor regulatory agencies worldwide. This may be due to the lack of practical protocols for the standards, and the misconceptions regarding the ease of use of CE, which could have hindered its widespread application. Although CE is an environmental friendly technique with minimal usage of toxic chemicals, few standard methods of CE exist in agriculture, environmental protection, food, beverage, chemical, and pharmaceutical industries in the United States, Britain, Europe, Japan, India, Brazil, Russia, and China. Since 2002, CE was used in our laboratory to analyze a large variety of samples. We found that once the CE method has been fully verified and described in detail, it was easily standardized. It is not necessary to screen the equivalent chromatographic column, or to use a specific liquid chromatographic (LC) column. This can effectively circumvent the challenge of shifting peak orders caused by different LC column selectivity. Once combined with general, high sensitivity detectors, CE can be used in the detection of bacteria or viruses in food safety, and play a greater role in the field of disease prevention and control. In the present review, applications of CE in nucleic acid detection for viruses and bacteria, analysis of vaccines, routine testing on food, dietary supplements, medical foods, cosmetics and disinfectants, proficiency tests, and emergency analyses of food poisoning were summarized. The applications and challenges of CE in the field of disease control and prevention were analyzed, and development of this technique was prospected.