The use of genetic modification (GM) in tree breeding would require that GM trees are superior to currently used seed orchard seedlings in the target trait and equal in other traits. We compare the variation of silver birch (Betula pendula Roth) lines carrying a sugar beet chitinase IV gene (chiIV) with the objective to improve fungal disease resistance to the variation of wild-type genotypes in disease resistance and other adaptive traits. The genetic variation in disease resistance was at the same level in transgenic (CVg 0.9–19.0%) and wild-type trees (CVg 0–19.7%), but the resistance characteristics of the most resistant wild-type genotype were usually equal or better than those of the best transgenic line. The broad-sense heritabilities varied from very low to moderate in disease resistance in both types. Broad-sense heritabilities in growth and leaf phenology-related traits were moderate and generally higher among the transgenic than the wild-type trees. The introduction of the sugar beet chiIV gene is likely to have fitness consequences in the form of lowered growth and quality characteristics of the transgenic lines without significant improvement in disease resistance compared with the natural variation of the same traits.