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Atypical motor patterns are potential early markers and predictors of later diagnosis of Autism Spectrum Disorder (ASD). This study aimed to investigate the early motor trajectories of infants at high-risk (HR) of ASD through MOVIDEA, a semi-automatic software developed to analyze 2D and 3D videos and provide objective kinematic features of their movements. MOVIDEA was developed within the Italian Network for early detection of Autism Spectrum Disorder (NIDA Network), which is currently coordinating the most extensive surveillance program for infants at risk for neurodevelopmental disorders (NDDs). MOVIDEA was applied to video recordings of 53 low-risk (LR; siblings of typically developing children) and 50 HR infants’ spontaneous movements collected at 10 days and 6, 12, 18, and 24 weeks. Participants were grouped based on their clinical outcome (18 HR received an NDD diagnosis, 32 HR and 53 LR were typically developing). Results revealed that early developmental trajectories of specific motor parameters were different in HR infants later diagnosed with NDDs from those of infants developing typically. Since MOVIDEA was useful in the association of quantitative measures with specific early motor patterns, it should be applied to the early detection of ASD/NDD markers.