Abstract Weather conditions during the growing season are determining the size and quality of the Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) Karst.) seed crop in northern areas. Pathogens, fungi, and insects also have an effect on seed crops. The varying quality of seeds from forest stands and seed orchards does not full fill the germination requirements of tree nurseries. Multi-phase pre-treatment are therefore used in forest tree seed centres to improve seed lots quality. The main objectives of this study were to analyse long-term variation in the size and quality of Scots pine seed crops in Northern Finland. Determine the impact of fungal injuries on the structures of Norway spruce seeds. To detect changes in the germination capacity and rate of Norway spruce seeds during pre-treatment phases and to determine the impacts of short-term and long-term storage on the germination of treated seeds. The study found that in most years, regeneration of Scots pine in Northern Finland is limited by quantity as well as quality the seed crop. The long-term average of the Scots pine seed crop was 77seeds/m2 and the long-term average expected germination percentage was 61%. Aeciospores of the inlad spruce cone rust Chrysomyxa pirolata (Körnicke) Wint. were found to form inside Norway spruce seeds, destroying the nucellar layers and reducing germination of seeds. In general, the germination capacity and rate of Norway spruce seeds increased during pre-treatment phases. The germination capacity of seeds increased about 30% and the rate by more than 40% during pre-treatment. During long-term storage the germination capacity and rate of pre-treated Scots pine seeds were preserved better in frozen storage than in cool storage. It was found that pre-treated Scots pine forest stand seeds can be stored for several years in frozen conditions. The germination capacity and rate of pre-treated orchard seeds were effected significantly more than those from forest stands. It is therefore recommended that Scots pine seeds from orchards be stored without pre-treatment. The germination capacity and rate of treated Norway spruce seeds from orchards was not significantly different after one year of storage.