The purpose of this study was the prospective comparison of objective and subjective effects of target volume region of interest (ROI) delineation using mouse–keyboard and pen–tablet user input devices (UIDs). The study was designed as a prospective test/retest sequence, with Wilcoxon signed rank test for matched-pair comparison. Twenty-one physician-observers contoured target volume ROIs on four standardized cases (representative of brain, prostate, lung, and head and neck malignancies) twice: once using QWERTY keyboard/scroll-wheel mouse UID and once with pen–tablet UID (DTX2100, Wacom Technology Corporation, Vancouver, WA, USA). Active task time, ROI manipulation task data, and subjective survey data were collected. One hundred twenty-nine target volume ROI sets were collected, with 62 paired pen–tablet/mouse–keyboard sessions. Active contouring time was reduced using the pen–tablet UID, with mean ± SD active contouring time of 26 ± 23 min, compared with 32 ± 25 with the mouse (p ≤ 0.01). Subjective estimation of time spent was also reduced from 31 ± 26 with mouse to 27 ± 22 min with the pen (p = 0.02). Task analysis showed ROI correction task reduction (p = 0.045) and decreased panning and scrolling tasks (p < 0.01) with the pen–tablet; drawing, window/level changes, and zoom commands were unchanged (p = n.s.) Volumetric analysis demonstrated no detectable differences in ROI volume nor intra- or inter-observer volumetric coverage. Fifty-two of 62 (84%) users preferred the tablet for each contouring task; 5 of 62 (8%) denoted no preference, and 5 of 62 (8%) chose the mouse interface. The pen–tablet UID reduced active contouring time and reduced correction of ROIs, without substantially altering ROI volume/coverage.