The invention features methods and compositions for diagnosis, including prognosis, of conditions associated with decreased arginine bioavailability (which can result from dysregulated arginine metabolism, e.g., due to increased arginase activity) by assessing in a sample from a subject the ratio of arginine to one or more, usually two or more, modulators of arginine bioavailability. In one embodiment, the ratio of arginine to (ornithine+citrulline) is assessed to aid in diagnosis.