A murmur is basically a sound that one hears when listening to the heart with a stethoscope. That sound is from the blood flowing between chambers in the heart and blood vessels near the heart. In many healthy individuals a sound can be heard, but the blood is flowing across totally normal valves and chambers. In up to 30 percent of normal children, a sound like this can be detected during a routine examination.
Abnormalities of the heart will also cause a doctor to hear a murmur. If there is a hole between the two sides of the heart and the blood is flowing across a space it normally does not go, it will cause a murmur. If there are abnormalities of the valves connecting the chambers of the heart, it can also cause a murmur.
Distinguishing between an "innocent" murmur and a murmur that indicates a significant heart abnormality is usually not difficult. There are certain characteristics of murmurs that help to differentiate the two: location, loudness, and pitch of the murmur, as well as what the rest of the heart exam sounds like.
Sometimes it can be a problem sorting out if the murmur represents an underlying problem or not just by listening with a stethoscope. The chest x-ray and EKG can help determine this. If it is still not clear, then an echocardiogram (a special ultrasound or sound wave test of the heart) can help define the exact anatomy of the heart.
In summary, I appreciate your concern, but try not to be alarmed. Your child's doctor will be happy to answer any questions that you have about the murmur.