In Scots pine (Pinus sylvestris L.), it has been shown that the parental conditions have a role in the phenological variation among first-year seedlings. For this reason, it is argued that they should be comprehensively controlled before estimating the parental genotype effects. This controlled-cross study examined the effects of a set of fathers of Scots pines on the timing of budset and autumn frost hardening of first-year seedlings. The paternal genotypes had either a northern or southern provenance, but had spent a period of over 25 years as grafts in a shared climatic environment in two closely located southern orchards. Pollen applied in the crosses was collected from these orchards in one year and all the maternal genotypes were pollinated in only one seed orchard. The results of freeze tests and budset observations of the consequent progeny were analysed and additionally compared with results obtained using seedlings from seed lots of natural forests in order to estimate the ability of northern paternal genotypes to maintain a northern effect under southern conditions. This environmentally controlled study demonstrated a significant effect of the paternal genotype on the budset and autumn frost hardening of first-year seedling of Scots pine. With the applied study design, no significant indication of an environmental influence on the effect of the paternal genotype was obtained. The accuracy of the observations is discussed. It is concluded that the results suggest a minor role of mutability in the effects of Scots pine paternal genotypes.