Hybrid aspen (Populus tremula L. × Populus tremuloides Michx.) plantations may produce valuable sawlogs for the growing timber market and contribute to carbon sequestration. However, environmental risks such as stem rot, the spread of which is facilitated by insect or frost damage, may reduce the proportion of valuable timber. It is important to understand the various factors affecting the spread of aspen rot to mitigate negative impacts with tree breeding. This study aimed to assess the impact of frost cracks and large poplar borer on stem rot in hybrid aspen clones in two clonal trials in Latvia. Genetic parameters for the traits were also estimated. The presence of insect passages substantially increased the probability of stem rot without distinct clonal differences. A negative and mainly insignificant correlation was observed between rot and stem cracking. The highest broad-sense heritability (H2 = 0.21) and strong site-site genotypic correlation (0.86) showed that the probability of stem rot is genetically determined in the study material. Significant differences in diameter at breast height, the presence of stem rot, and its severity were found among the clones, albeit without undesirable positive correlation between growth and presence of decay. This indicated its potential to improve both productivity and rot resistance.