Many neurological diseases, such as Parkinson's disease and epilepsy, can significantly impair the motor function of the patients, often leading to a dramatic loss of their quality of life. Human motion analysis is regarded as fundamental towards an early diagnosis and enhanced follow-up in this type of diseases. In this contribution, we present NeuroKinect, a novel system designed for motion analysis in neurological diseases. This system includes an RGB-D camera (Microsoft Kinect) and two integrated software applications, KiT (KinecTracker) and KiMA (Kinect Motion Analyzer). The applications enable the preview, acquisition, review and management of data provided by the sensor, which are then used for motion analysis of relevant events. NeuroKinect is a portable, low-cost and markerless solution that is suitable for use in the clinical environment. Furthermore, it is able to provide quantitative support to the clinical assessment of different neurological diseases with movement impairments, as demonstrated by its usage in two different clinical routine scenarios: gait analysis in Parkinson's disease and seizure semiology analysis in epilepsy.