Abstract Objectives To compare magnetic resonance imaging–targeted biopsy (MRITB) and conventional transrectal ultrasound–guided biopsy (TRUSGB) in the detection of prostate cancer (PCa) at our institution. Methods Our prospective registry of patients undergoing prostate MRITB from December 2010 to July 2013 was analyzed. Patients were matched one-to-one to patients who underwent TRUSGB based on the following characteristics: age, prostate-specific antigen level, prostate volume, race, family history of PCa, initial digital rectal examination (DRE), prior use of 5-alpha reductase inhibitor, and prior diagnosis of PCa. MRITB was performed using a TargetScan system with the patient under general anesthesia. Magnetic resonance imaging suspicious regions (MSRs) were targeted with cognitive registration, and a full TargetScan template biopsy (TSTB) was also performed. Results In total, 34 MRITB patients were matched individually to 34 TRUSGB patients. As compared with TRUSGB, patients who underwent MRITB had a greater overall rate of PCa detection (76% vs. 56%, P = 0.12) and a significantly higher number with Gleason score≥7 (41% vs. 15%, P = 0.03), whereas the rates of Gleason score 6 PCa detection were similar between MRITB and TRUSGB (35% vs. 41%, P = 0.80). As compared with the TSTB, magnetic resonance imaging suspicious regions–directed biopsies during MRITB had a significantly higher overall PCa detection (54% vs. 24%, P <0.01) and Gleason score≥7 PCa detection (25% vs. 8%, P <0.01). When compared with TSTB, TRUSGB had similar detection rates for benign prostate tissue (76% vs. 79%, P = 0.64), Gleason score 6 PCa (16% vs. 14%, P = 0.49), and Gleason score ≥7 PCa detection (8% vs. 7%, P = 1.0). Conclusions Cognitive registration MRITB significantly improves the detection of Gleason score≥7 PCa as compared with conventional TRUSGB.