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It has been suggested that abortion of ovules in perennials is caused partly by early acting genetic load (abortions due to ‘bad offspring’). However, it is still unclear what proportion of abortions of naturally pollinated seeds are due to early genetic load. Here we suggest that variation between maternal genotypes (abortions due to ‘bad maternal genotypes’) may be an even more important factor causing genetic abortions than early load, based on results from Scots pine. The early load is severe in Scots pine: in experimental self-pollinations on average 76% of the seeds were aborted. Comparison of naturally pollinated and experimentally cross-pollinated seeds showed that the abortion rate of naturally pollinated seeds was only slightly, and not statistically significantly, higher than that of experimentally cross-pollinated seeds (30% vs. 26.5%, respectively). Thus, although early load can be high under self-pollination in Scots pine, it does not account for a high share of abortions of naturally pollinated seeds. Instead, maternal genotype determined the seed abortion rate: in a separate experiment using an experimental population (clonal stand), 29% of the total variance in seed abortion was due to variation between maternal genotypes. We studied further whether ‘bad maternal genotypes’ could be explained by trade-offs between seed abortion and other fitness functions. Only one statistically significant genetic correlation was found, a positive association between cone production and successful seed development. Thus ‘bad maternal genotypes’ aborted a higher proportion of their seed and produced less cones than the ‘good maternal genotypes’.