Large amounts of certain vitamins or colored juice can affect the color of urine. Urine color is also affected by it's concentration. If he's drinking only juice with no water urine can become more concentrated and appear darker.
Vitamins, when they affect the urine tend to make urine brighter in color. Food dyes of any kind can affect the urine's color and odor in sufficient quantities.
However, it should not be assumed that juices or foods are the cause. The next time his urine appears dark, call the Doctor and provide a specimin. Some simple tests can then be done to rule out things like blood or sugar in the urine. A visit to the Doctor may or may not be required, but keep track of any changes between checkups.
Whether juice is the specific cause in his urine changes or not, juices should be limited to 4-6 ounces of juice daily, according to the AAP. Make sure any juice you give him is "no sugar added".
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