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A bio-anatomical quality assurance (QA) method employing tumor control probability (TCP) and normal tissue complication probability (NTCP) is described that can integrate radiobiological effects into intensity-modulated radiation therapy (IMRT). We evaluated the variations in the radiobiological effects caused by random errors (r-errors) and systematic errors (s-errors) by evaluating TCP and NTCP in two groups: patients with an intact prostate (G(intact)) and those who have undergone prostatectomy (G(tectomy)). The r-errors were generated using an isocenter shift of ±1 mm to simulate a misaligned patient set-up. The s-errors were generated using individual leaves that were displaced inwardly and outwardly by 1 mm on multileaf collimator field files. Subvolume-based TCP and NTCP were visualized on computed tomography (CT) images to determine the radiobiological effects on the principal structures. The bio-anatomical QA using the TCP and NTCP maps differentiated the critical radiobiological effects on specific volumes, particularly at the anterior rectal walls and planning target volumes. The s-errors showed a TCP variation of -40-25% in G(tectomy) and -30-10% in G(intact), while the r-errors were less than 1.5% in both groups. The r-errors for the rectum and bladder showed higher NTCP variations at ±20% and ±10%, respectively, and the s-errors were greater than ±65% for both. This bio-anatomical method, as a patient-specific IMRT QA, can provide distinct indications of clinically significant radiobiological effects beyond the minimization of probable physical dose errors in phantoms.