Much progress has been made in pesticide analysis over the past decade, during this time hyphenated techniques involving highly efficient separation with sensitive detection have become the techniques of choice. Among these, methods based on separation with mass spectrometric detection have resulted in greater likelihood of identification and are acknowledged to be extremely useful and authoritative methods for the determination of pesticide residues but the inherent advantages of the use of CE as a separation technique are well-known and can be summarized as high separation efficiency, low analysis time, high resolution power, and low consumption of samples and reagents. Although UV is the most widely used detector in CE equipments so far so this detection mode is also included for the review. Even with such powerful instrumental techniques, however, the risk of interference increases with the complexity of the matrix studied, so sample preparation is often the limiting step in systems before instrumental analysis and is still mandatory in many applications, for example, food analysis. This article summarizes the analytical characteristics of the different methods of sample preparation for the determination of pesticide residues in a variety of food matrices, and surveys their recent applications in combination with CE using UV and MS detectors. We will discuss the advantages and the disadvantages of different methods, the instrumental aspects, summarize and conclude the perspectives for the future.