Diseases caused by Ganoderma boninense are considered the greatest threat to sustainable palm oil production in SE Asia but the host-pathogen interaction has not been fully investigated at the cellular level. The pathogen growing from colonised blocks as small as 3cm3 could successfully infect oil palm seedlings provided the inoculum was attached to the roots. Reproducible infection of roots with an aggressive isolate GMR3 showed penetration and infection of intact roots, followed by rapid progression throughout the root and then colonization of the lower stem (bole). Transmission electron microscopy showed invasion of the root cortex, with no evidence of selective progression through the vascular system or lacunae. In newly colonised tissue, the fungus appeared as a hemibiotroph, with numerous large hyphae occupying entire cells. In the bole, this led to a complete depletion of previously abundant starch grains. Subsequently, in the roots and colonized bole widespread, necrotrophic, enzymatic attack of all layers of the host cell walls occurred. A third developmental stage was the formation of an extensive, melanized, tough mycelium or pseudo-sclerotium which surrounded roots and comprised many very thick-walled cells. Macroscopic observation of the bole of randomly felled, commercial palms provided confirmatory evidence that multiple infections originated in the roots before spreading into the palm base. The pathogen did not grow well in soil (except when sterilised) and is therefore unlikely to spread from palm to palm by mycelial extension. It is likely to remain in debris to avoid competition from natural soil microflora. The field implications of these studies is discussed.