Cerebral palsy (CP) is the major cause of physical disability in childhood and often progress in motor control and changes in the functional level are affected by the difficulty to acquire, process and recall information. Animal models have shown that stress interferes with these processes and that exposure to hypoxia, low birth weight and prematurity leads to alterations in the hypothalamic-pituitary-adrenal (HPA) axis and the sympathetic response. The main objective of this research was toestimate and associate stress levels of children with CP before and after physiotherapy intervention focused on the acquisition of motor skills. A total of 86 subjects were recruited, between 6 months and 6 years old. 41 of them had CP and the physiotherapy intervention was at the OrtopediaInfantil Roosevelt Institute or in Aconiños Association. The other 45 subjects were healthy children (CG) matched by age, gender and time of sampling. The measurements by cortisol and alpha amylase were performed by electrochemiluminescence and spectrophotometry methods. In this research only significant differences for cortisol concentrations in subjects with CP relative to GC were found (P=0.009). And a reduction in these levels 20 minutes post intervention (P < 0.05). These data are the first report on the performance of biomarkers of stress in children with CP and evidence alterations of hypothalamic pituitary adrenal axis in children with CP, as well as the influence of a physiotherapy session in the modifications of these levels.