The HortResearch Apple Genetics Population mainly consisting of families derived from open-pollinated cultivars from around the world, was evaluated for resistance to apple scab, fire blight, and woolly apple aphid. Large scale patterns and clumping were present in the distributions of pest and diseases, but the experimental design of randomised incomplete blocks was found to adequately accommodate them. From the variance components, estimated using restricted maximum likelihood (REML), heritabilities and combining abilities were computed. In some cases where the data showed a skewed distribution, jackknife estimates of the standard errors for the heritabilities were derived. The combining abilities were ranked, and the confidence intervals for each rank determined by bootstrapping the residuals. The heritability for apple scab resistance was about 0.35, although it was much lower for some sub-populations due to high frequencies of resistant seedlings. Similarly, heritability for fire blight resistance was 0.10 for subline 94, while they were 0.29 for subline 92, and 0.70 for subline 93. The preliminary estimate for woolly apple aphid resistance in subline 93 was 0.52. Test-crosses confirmed the presence of major gene resistances to this pest in the open-pollinated seedlings derived from 'David', 'Korichnoe Polosatoje', Mildew Immune Seedling, and M. floribunda 821. Analysis of the infestation data on the Kazak accessions suggested a strong genetic component in the differences for the apple leaf curling midge, but not for the light brown apple moth.