Recent changes to the patient note (PN) format of the United States Medical Licensing Examination have challenged medical schools to improve the instruction and assessment of students taking the Step-2 clinical skills examination. The purpose of this study was to gather validity evidence regarding response process and internal structure, focusing on inter-rater reliability and generalizability, to determine whether a locally-developed PN scoring rubric and scoring guidelines could yield reproducible PN scores. A randomly selected subsample of historical data (post-encounter PN from 55 of 177 medical students) was rescored by six trained faculty raters in November-December 2014. Inter-rater reliability (% exact agreement and kappa) was calculated for five standardized patient cases administered in a local graduation competency examination. Generalizability studies were conducted to examine the overall reliability. Qualitative data were collected through surveys and a rater-debriefing meeting. The overall inter-rater reliability (weighted kappa) was 0.79 (Documentation = 0.63, Differential Diagnosis = 0.90, Justification = 0.48, and Workup = 0.54). The majority of score variance was due to case specificity (13%) and case-task specificity (31%), indicating differences in student performance by case and by case-task interactions. Variance associated with raters and its interactions were modest (<5%). Raters felt that justification was the most difficult task to score and that having case and level-specific scoring guidelines during training was most helpful for calibration. The overall inter-rater reliability indicates high level of confidence in the consistency of note scores. Designs for scoring notes may optimize reliability by balancing the number of raters and cases.