In Sulawesi, Indonesia, cocoa smallholdings are seriously affected by the cocoa pod borer (Conopomorpha cramerella, CPB). CPB is detrimental to both cocoa production and bean quality, and is a major concern to cocoa smallholders, processors, exporters and the international market. An Australian Centre for International Agricultural Research (ACIAR)-funded project was initiated to develop a locally applicable, farmer-participatory methodology for selecting and testing promising cocoa genotypes on farms. In a trial established on a farm in SouthEast Sulawesi, local Indonesian and international cocoa selections were propagated clonally by side-grafting onto mature trees of mixed genotype and evaluated for 2 years for pod value, quality and resistance to pest/diseases. Local selections were based on the observations of farmers, extension officers or researchers and included a number of clones specifically selected for resistance (or susceptibility, as checks) to CPB. Our results on the CPB-infestation of 34 clones in the trial indicate the potential of employing on-farm selection and testing to improve cocoa farms. Severity of infestation was determined in ripe pods according to whether the proportion of beans damaged by CPB larvae was light (less than 10%), moderate (10-50%) or severe (over 50%). Total CPB incidence in ripe pods for most of the clones was high, exceeding 75%, and was correlated with severe and light incidence, both of which varied more. The data support a model that predicts severe infestation inflicting bean losses occurs above a critical threshold of total CPB incidence. The cumulative CPB incidence in infested pods was significantly lower in a local selection, Aryadi 2, which also had fewer larval entry holes and a low exit/entry ratio indicating a degree of resistance to CPB. The incidence of lightly infested pods was significantly lower in the susceptible controls. Pod hardness was moderately high in Aryadi 2. However, VSD3 (a local selection), Scavina12, KKM22 and BR25, had low levels of severe infestation and/or high incidences of light infestation, but had relatively soft pods. This suggests that factors in addition to pod hardness might be involved in resistance, a possibility also supported by the positive correlation of CPB incidence in ripe pods with that in immature pods and the larger seasonal fluctuations of CPB incidence observed in resistant clones, compared to susceptible clones. In a mixed genotype stand, the lower CPB incidence observed in some clones might be explained partly by pest non-preference.