Ayurveda and modern medicine differ in one basic sense: Modern Medicine is driven by Structure or the 'Part' and is thus substantially dependent on laboratory tests and diagnostic investigations such as x-ray, scans, etc., in the diagnosis process as well as the basis of medical management. But, Ayurveda gives importance to Function or the effect of the 'Whole' . When every sub-system functions properly, it is health. When there is some difference or difficulty in the function, ill-health is caused. That is why functional behaviour, expressed as symptoms, constitutes the basis of both diagnosis, as well as medical management, in Ayurveda. Which is why, it is said that modern medicine is disease-centric , while Ayurveda is patient-centric.
There need not be any contradiction between Ayurveda and Modern Medicine. The two systems may truly and effectively complement each other, when structural knowledge is judiciously integrated and interpreted in the Ayurveda paradigm of 'whole person' functional performance.
Contrary to common perception, through the ages, the seers of Ayurveda recognized the need to ensure that Ayurveda was relevant to contemporary needs and developments. Vagbhata, the latest of the acharyas, says in his text that he is trying to make the system up-to-date and suitable for the times (yuganuroopa). The practice of Ayurveda being reduced to a system of prescribed and ‘over the counter' medication, akin to Allopathic medicines, is not the answer. The changes are to be only in application, not in principles. Thus, one can apply modern tools, modern insight, and modern knowledge, whether it is at the biological, anatomical, physiological, or genetic level, in the context of Ayurveda's foundational principles, without any contradiction whatsoever. Further, modern advances in risk management, emergency management, organ transplantation, and surgical interventions of all types can only complete and enhance the value of Ayurveda and in no way detract from it.
One may posit that for early to mature stages as well as chronic stages of a disease, Ayurveda has excellent answers to the health needs of mankind; while once a person has already reached an acute or emergency health state, modern medicine and surgical technique with attendant medical technologies is unparalleled in its effectiveness.
from this site: http://ayurvaid.com/AyurVaid/?q=ayurveda-vis-a-vis-modern-medicine