An on-line microdialysis sampling coupled with flow injection (FI) electrothermal atomic absorption spectrometry (ETAAS) method has been developed for in vivo monitoring of extracellular diffusible Mn in brains of living rats. Microdialysates perfused through implanted microdialysis probes were collected with a sample loop of an on-line injection valve and directly introduced into the atomizer of the ETAAS by a FI system. Ultrapure saline solution (0.9% NaCl) was used as the perfusion solution at a flow rate of 1 µl min−1 through the microdialysis probe. The 25 µl of chemical modifier [0.4 g l−1 of Mg(NO3)2] and 25 µl of microdialysate were on-line mixed at a micro-Tee and loaded into a sample loop. A six-port on-line injection valve equipped with a 50 µl of sample loop, a peristaltic pump and an autosampler arm of ETAAS for direct introduction of the sample into the graphite tube were employed to act as a homemade FI system. The optimized conditions of ETAAS were performed for measurement of Mn in microdialysate. The performance characteristics of the on-line microdialysis-FI-ETAAS system for Mn were as follows: linearity range, 0–20 ng ml−1; detection limit (3σ, n = 7), 0.43 ng ml−1; recovery (n = 3), 98%–114%; precision (RSD, n = 20), 7.2%. The accuracy of the proposed on-line method was checked by four spiked artificial cerebrospinal fluid samples and compared with conventional ETAAS. The use of an on-line microdialysis-FI-ETAAS system permitted the in situ, dynamic and continuous in vivo monitoring of extracellular diffusible Mn in brains of living anaesthetized rats after administrated with MnCl2 with a temporal resolution of 25 min.