This paper explores some of the conceptual issues that arise when comparing homeopathy with the mainstream medical system, both in terms of their underpinning philosophies and in their treatment methods, and especially when applied to the problem of cancer. A review is under-taken of the key concepts that underpin both medical approaches: the holistic approach of homeopathy and the reductionist approach of mainstream medicine. The article closes with a discussion of the emerging conflicts between classical homeopathy and the Banerji protocols.