Adeno-associated virus (AAV) mediated micro-dystrophin gene therapy holds great promise for treating Duchenne muscular dystrophy (DMD). Previous studies have revealed excellent skeletal muscle protection. Cardiac muscle is also compromised in DMD patients. Here we show that a single intravenous injection of AAV serotype-9 (AAV-9) micro-dystrophin vector efficiently transduced the entire heart in neonatal mdx mice, a dystrophin-deficient mouse DMD model. Furthermore, micro-dystrophin therapy normalized the heart rate, PR interval and QT interval. Cardiomyopathy index was also significantly improved in treated mdx mice. Our study demonstrates for the first time that AAV micro-dystrophin gene therapy can ameliorate the electrocardiographic abnormalities in a mouse model for DMD.