Background: Pharmacokinetic (PK) models can describe microvascular density and integrity. An essential component of PK models is the arterial input function (AIF) representing the time-dependent concentration of contrast agent (CA) in the blood plasma supplied to a tissue. Purpose/Hypothesis: To evaluate a novel method for subject-specific AIF estimation that takes inflow effects into account. Study Type: Retrospective study. Subjects: Thirteen clinical patients referred for spine-related complaints; 21 patients from a study into luminal Crohn's disease with known Crohn's Disease Endoscopic Index of Severity (CDEIS). Field Strength/Sequence: Dynamic fast spoiled gradient echo (FSPGR) at 3T. Assessment: A population-averaged AIF, AIFs derived from distally placed regions of interest (ROIs), and the new AIF method were applied. Tofts' PK model parameters (including vp and Ktrans) obtained with the three AIFs were compared. In the Crohn's patients Ktrans was correlated to CDEIS. Statistical Tests: The median values of the PK model parameters from the three methods were compared using a Mann–Whitney U-test. The associated variances were statistically assessed by the Brown-Forsythe test. Spearman's rank correlation coefficient was computed to test the correlation of Ktrans to CDEIS. Results: The median vp was significantly larger when using the distal ROI approach, compared to the two other methods (P < 0.05 for both comparisons, in both applications). Also, the variances in vp were significantly larger with the ROI approach (P < 0.05 for all comparisons). In the Crohn's disease study, the estimated Ktrans parameter correlated better with the CDEIS (r = 0.733, P < 0.001) when the proposed AIF was used, compared to AIFs from the distal ROI method (r = 0.429, P = 0.067) or the population-averaged AIF (r = 0.567, P = 0.011). Data Conclusion: The proposed method yielded realistic PK model parameters and improved the correlation of the Ktrans parameter with CDEIS, compared to existing approaches. Level of Evidence: 3. Technical Efficacy Stage 1. J. Magn. Reson. Imaging 2018;47:1197–1204.@en