The objective of this study was to investigate the altitudinal variation within and between Scots pine (Pinus sylvestris L.) populations in Turkey using 23 morphological characters. Seeds were collected from 149 open-pollinated parents (trees) from five populations sampled from different altitudes in the natural distribution range of the species in northern Turkey and raised in a nursery along the coast. The populations were compared based on phenotypic variation of cones, seeds, seed-wings, juvenile seedlings and seedlings morphology, to study the pattern of natural variation of the species. ANOVA and Duncan test showed that the morphological characters differed by populations. Also, the cluster modeling performed on the morphological characters suggested that altitude was a major factor to differentiate the groups. This study showed that there were significant differences within and between the populations in P. sylvestris for the morphologic characters studied.