Purpose-To compare the toxicity and biochemical outcomes of intensity-modulated radiation therapy (IMRT) and 125 I transperineal permanent prostate seed implant ( 125 I) for patients with lowrisk prostate cancer.Methods and Materials-Between 1998 and 2004, a total of 374 low-risk patients (prostatespecific antigen < 10 ng/ml, T1c-T2b, Gleason score of 6 or less, and no neoadjuvant hormones) were treated at Fox Chase Cancer Center (216 IMRT and 158 125 I patients). Median follow-up was 43 months for IMRT and 48 months for 125 I. The IMRT prescription dose ranged from 74-78 Gy, and 125 I prescription was 145 Gy. Acute and late gastrointestinal (GI) and genitourinary (GU) toxicity was recorded by using a modified Radiation Therapy Oncology Group scale. Freedom from biochemical failure was defined by using the Phoenix definition (prostate-specific antigen nadir + 2.0 ng/ml).Results-Patients treated by using IMRT were more likely to be older and have a higher baseline American Urological Association symptom index score, history of previous transurethral resection of the prostate, and larger prostate volumes. On multivariate analysis, IMRT was an independent predictor of lower acute and late Grade 2 or higher GU toxicity and late Grade 2 or higher GI toxicity. Three-year actuarial estimates of late Grade 2 or higher toxicity were 2.4% for GI and 3.5% for GU by using IMRT compared with 7.7% for GI and 19.2% for GU for 125 I, respectively. Four-year actuarial estimates of freedom from biochemical failure were 99.5% for IMRT and 93.5% for 125 I (p = 0.09).Conclusions-The IMRT and 125 I produce similar outcomes, although IMRT appears to have less acute and late toxicity.