Purpose This study was a 12-month prospective investigation of changes in the medial gastrocnemius (MG) muscle morphology in children aged 2-5 years with spastic cerebral palsy (CP) who had received no previous intramuscular injections of botulinum neurotoxin type-A (BoNT-A) and were randomised to receive either single or multiple (three) BoNT-A injections to the gastrocsoleus. MG morphological changes were compared to age-matched typically developing (TD) peers. Methods Thirteen children with spastic CP with a mean age of 45 (15) months and 18 TD children with a mean age of 48 (14) months participated in the study. The principal outcome measures were MG muscle volume, fascicle length, pennation angle and physiological cross-sectional area (PCSA), which were obtained using 2D and 3D ultrasound. Results The single and multiple injection frequency groups significantly increased MG muscle volume at 12 months relative to the baseline by 13 and 15 %, respectively. There were no significant differences in the MG muscle volume 28.5 (12.3) versus 30.3 (3.8) ml, fascicle length 48.0 (10.4) versus 44.8 (1.2) mm or PCSA 7.0 (1.2) versus 6.6 (1.7) cm2 between the single and multiple injection groups, respectively, at 12 months follow-up. The change in MG muscle volume in the single and multiple injection groups was significantly lower than the TD peers by 66 and 60 %, respectively. Interpretation In young children with spastic CP, naive to BoNT-A treatment, MG muscle growth over 12 months does not appear to be influenced by intramuscular BoNT-A injection frequency. However, MG muscle growth in the spastic CP groups was significantly lower than the age-matched TD peers. It is unclear whether this is an effect of intramuscular BoNT-A injections or reduced growth rates in children with spastic CP in general. Controlled investigations and longitudinal studies with multiple measurement time points are required in order to determine the influence of BoNT-A treatment on muscle physiological and mechanical growth factors in young children with spastic CP.