Deformational plagiocephaly (DP) is considered a risk factor for facial asymmetry. This cohort-based, prospective, follow-up study used three-dimensional (3D) stereophotogrammetry to assess the development of facial asymmetry in a normal birth cohort and to investigate the impact of DP on facial asymmetry for the age range of one to three years. The study sample consisted of 75 children: 35 girls (47%) and 40 (53%) boys recruited from Oulu University Hospital. A total of 23 (31%) subjects had a history of DP in infancy. 3D facial images were obtained at the mean (SD) age of 1.01 (0.04) year old at T1 and 3.02 (0.14) years old at T2. To determine facial asymmetry, both landmark-based and surface-based facial symmetry methods were used. As measured with the surface-based methods, upper facial symmetry improved from T1 to T2 (p < 0.05). As measured with the landmark-based methods, facial symmetry improved on the upper and lower jaw from T1 to T2 (p < 0.05). The asymmetric effect of DP on the upper parts of the face tends to correct spontaneously during growth. Results indicate that previous DP does not seem to transfer to facial or occlusal asymmetry at the age of three years old.