Background :Although modern whole-exome sequencing (WES) kits are widely used, their ability to capture regulatory UTRs and maintain uniform coverage across targeted regions varies substantially. Understanding these differences is essential for analyses involving 5′-UTRs and 3′-UTRs, particularly in studies of non-coding variation that may influence splicing. Target-enrichment performance was compared across four major WES design kits' providers: Roche/NimbleGen, Agilent SureSelect, IDT xGen, and Twist Bioscience. The analysis focused separately on coding sequences (CDS), 5′-UTRs, and 3′-UTRs. Capture efficiency was measured as the proportion of genomic bases covered at least once, standardized by the relative size of each region represented in the kit design to enable fair comparisons. Coverage behavior along the length of each sequence was evaluated using normalized sequence lengths (0–100), equal-sized bins, and area-standardized coverage curves, with additional stratification by log2-based sequence-length quantiles. Finally, common metrics such as mean coverage were also compared. While newer kits showed similar performance in raw metrics (capture efficiency and mean coverage), significant differences emerged after region-length standardization. Several kits appeared to perform well only because their designs excluded substantial portions of UTRs. Length-normalized profiles further revealed kit-specific coverage-decay patterns along targeted regions. Moreover, a significant decline in coverage efficiency near boundary regions was observed, as genomic fragments's length increases. In summary, WES kits differ not only in the extent of the regions they target, but also in how coverage is distributed along sequence length.