Altogether 197 grafts were studied in Pauska seed orchard in South-Estonia to find out the effect of the fertilization on Norway spruce grafts. The fertilization trials were carried out in May 1988 and 2006. The grafts of 4 different clones with 5 different fertilization treatments (N, P, K, NPK, control) were under study. The effect of three factors (fertilization, clone and year) on different characteristics of spruce grafts was studied. The linear methods with R software were used to find out relationships between variables. In addition to the morphological features and the content of nutrients in needles, the quantities and qualities of the mean cone and the weight of 1000 seeds were measured. Furthermore, the variation of quantities of needles (density, weight, length) and the content of nutrients in needles between years 1988 and 2007 were compared, using the linear methods with R software package. The morphological characteristics and nutrient content of needles, the mass of cones and seeds have depended the most on a calendar year. During the last research period (2003−2007), the needles of grafts under study were longer, lighter and with lower density compared to earlier research period (1988-1993). The effect of a clone was also essential. Needles of younger grafts were longer, heavier and set sparser than needles of older grafts. The needle nutrient content of younger grafts was also higher compared to the older ones. The effect of fertilizers on the grafts was dependent on the period of time. Nitrogen fertilizers increased the N-content in their needles during the first four years and also after repetitive fertilization. Phosphate fertilizers increased the P-content in their needles starting from the third year after their fertilization. The impact of potassium fertilizers on the K-content of their needles appeared 2−4 years after their fertilization. Combined fertilizers increased the N- and P-content in the needles to some extent, whereas it decreased their Ca- and Mg-content.