JChainsAnalyser is a Java-based program for the analysis of two-dimensional images of magneto-rheological fluids (MRF) at low concentration of particles obtained using the video-microscopy technique. MRF are colloidal dispersions of micron-sized polarizable particles in a carrier fluid with medium to low viscosity. When a magnetic field is applied to the suspension, the particles aggregate forming chains or clusters. Aggregation dynamics [P. Domínguez-García, S. Melle, J.M. Pastor, M.A. Rubio, Phys. Rev. E 76 (2007) 051403] and morphology of the aggregates [P. Domínguez-García, S. Melle, M.A. Rubio, J. Colloid Interface Sci. 333 (2009) 221–229] have been studied capturing images of the fluid and analyzing them by using this software. The program allows to analyze automatically the MRF images by means of an adequate combination of different imaging methods, while magnitudes and statistics are calculated and saved in data files. It is possible to run the program on a desktop computer, using the GUI (graphical user interface), or in a cluster of processors or remote computer by means of command-line instructions.