In this paper, we present MD-TRACKS, an advanced statistical analysis toolkit for Molecular Dynamics and Monte Carlo simulations. The program is compatible with different molecular simulation codes, and the analysis results can be loaded into spreadsheet software and plotting tools. The analysis is performed with commands that operate on a binary trajectory database. These commands process not only plain trajectory data but also the output of other MD-TRACKS commands, which enables complex analysis work flows that are easily programmed in shell scripts. The applicability, capabilities, and ease of use of MD-TRACKS are illustrated by means of examples, that is, the construction of vibrational spectra and radial distribution functions from a molecular dynamics run is discussed in the case of tetrahydrofuran. These properties are compared with the experimental data available in the literature. MD-TRACKS is open-source software distributed at http://molmod.ugent.be/code/.