The presence of abnormal infant General Movements (GMs) is a strong predictor of progressive neurodevelopmental disorders, including cerebral palsy (CP). Automation of the assessment will overcome scalability barriers that limit its delivery to at risk individuals. Here, we report a robust markerless pose estimation scheme, based on advanced deep learning technology, to track infant movements in consumer mobile device video recordings. Two deep neural network models, namely Efficientnetb6 and resnet152, were trained on manually annotated data across twelve anatomical locations (3 per limb) in 12 videos from 6 full term infants (mean age = 17.33 (SD 2.9) wks, 4 male, 2 female), using the DeepLabCut framework. Kfold cross validation indicates the generalization capability of the deep nets for GM tracking on out of domain data with an overall performance of 95.52% (SD 2.43) from the best performing model (Efficientnetb6) across all infants (performance range: 84.32 to 99.24% across all anatomical locations). The paper further introduces an automatic, unsupervised strategy for performance evaluation on extensive out of domain recordings through a fusion of likelihoods from a Kalman filter and the deep net. Findings indicate the possibility of establishing an automated GM tracking platform, as a suitable alternative to, or support for, the current observational protocols for early diagnosis of neurodevelopmental disorders in early infancy.