OBJECTIVE Bioelectrical impedance analysis is a promising method in determining the body compartments in haemodialysis patients. In this study, we aimed to investigate the agreement between two widely used methods: the single-frequency and multi-frequency bioelectrical impedance analyses. METHODS Maintenance haemodialysis patients were enrolled in the study. Single-frequency and multi-frequency bioelectrical impedance analyses were performed consecutively before haemodialysis. A second bioelectrical impedance analysis was performed right after the haemodialysis session. A third bioelectrical impedance analysis was performed one hour after haemodialysis. We used weight change as a measure of fluid removal during haemodialysis session. RESULTS Bioelectrical impedance analysis estimates from both devices had significant differences. Best agreement was observed between single frequency and multifrequency devices' extracellular water estimates immediately after haemodialysis (mean difference 0.076 L). We found the best agreement between weight change and extracellular water change using single-frequency bioimpedance analysis. Moreover, one hour waiting time did not improve the agreement between weight and extracellular water changes for both devices. Different estimates seem to be caused by different raw impedance data measured by both devices and device-specific equations. CONCLUSIONS There are significant differences among bioelectrical impedance measurements performed with different bioelectrical impedance analyzers. Using open source software might be an important step forward in the development of standardized measurements.