Detection of anomalous trajectories is an important problem with potential applications to various domains, such as video surveillance, risk assessment, vessel monitoring and high-energy physics. Modeling the distribution of trajectories with statistical approaches has been a challenging task due to the fact that such time series are usually non stationary and highly dimensional. However, modern machine learning techniques provide robust approaches for data-driven modeling and critical information extraction. In this paper, we propose a Sequence to Sequence architecture for real-time detection of anomalies in human trajectories, in the context of risk-based security. Our detection scheme is tested on a synthetic dataset of diverse and realistic trajectories generated by the ISL iCrowd simulator [11,12]. The experimental results indicate that our scheme accurately detects motions that deviate from normal behaviors and is promising for future real-world applications.