Background: Little is known about electrical remodeling of the native conduction systems, particularly how the PR interval changes, after cardiac resynchronization therapy (CRT). We investigated the effects of CRT on the intrinsic PR interval (i-PRi) and QRS duration (i-QRSd). Methods and results: In 100 consecutive CRT recipients with sinus rhythm and long-term follow-up (>1 year), the i-PRi and i-QRSd were measured at baseline and at the last echocardiographic follow-up (33.4 ± 17.9 months) with biventricular pacing temporarily withdrawn. The relative decrease in the left ventricular end-systolic volume (LVESV) was measured to define CRT-responders (≥15%) and super-responders (≥30%). Following CRT, the left ventricular (LV) ejection fraction increased significantly (p < 0.001). In CRT-responders (n = 71), the LVESV and i-QRSd decreased markedly (170 ± 39 to 159 ± 24 ms, p = 0.012). However, the i-PRi was not shortened with CRT response and was actually likely to increase, even in the super-responder group (n = 33). Moreover, lengthening of the i-PRi was observed consistently irrespective of the CRT response status, beta-blocker use, or amiodarone use. CRT non-responders were associated with a remarkable PR prolongation (p = 0.005) and QRS widening (p = 0.001), along with positive ventricular remodeling. Conclusion: LV volume and i-QRSd decreased markedly with CRT response. However, the i-PRi was not shortened, but rather increased regardless of the degree of CRT response. CRT non-response was associated with a considerable increase in the i-PRi and i-QRSd, along with positive ventricular remodeling. CRT-induced electrical reverse remodeling might occur preferentially in the intraventricular, but not the atrioventricular, conduction system.