This study observed the genotypic variation among Scots pine (Pinus sylvestris L.) half-sib families’ susceptibility to Heterobasidion annosum. Scots pine susceptibility was tested in 12 half-sib families by inoculating them with four different H. annosum strains. At two, six, and ten months after the inoculations, the susceptibility indicators (incidence rate, pathogen spread, and mortality rate) were compared and the total phenolic compounds (TPC) in the inoculated and control groups determined using the Folin–Ciocalteu method. Among half-sib families, significant differences were found for seedling mortality (range: 1.3%–21.2%); however, the differences in incidence rate (range: 54%–77%) and pathogen spread (range: 24–53 mm) were not significant. The incidence rate among half-sib families correlated positively and significantly (r = 0.72, p < 0.05) with the mortality rate, while the pathogen spread correlated negatively with mortality, although the correlation was not significant (r = −0.29, p > 0.05). The TPC comparison with susceptibility indicators showed that the half-sib families with lower susceptibility were characterized by the ability to increase TPC after inoculation compared to the control group. This tendency was most apparent in stems and roots six and two months after inoculation, respectively. Correlation analyses revealed that higher TPC in stems six months after inoculation determined a lower incidence rate (r = −0.32, p < 0.05), while higher Change in concentration of total phenolic compounds (TPCΔ) indicated a lower pathogen spread (r = −0.60, p < 0.05). The lowest incidence of the pathogen was determined in half-sib families with the highest TPCΔ in the roots two months after inoculation. The lower susceptibility of Scots pine half-sib families is based on a combination of enhanced constitutive and inducible phenolic defense mechanisms. The data may facilitate the selection of Scots pine half-sib families with low susceptibility for breeding programs and forest management strategies.