The onset of a therapeutic response to antidepressant treatment exhibits a delay of several weeks. The present study was designed to know whether extracellular serotonin (5-HT) levels need to be increased in territories of 5-HT innervation in order to obtain beneficial effects from a chronic treatment with a serotonin-selective reuptake inhibitor (SSRI). Thus, we performed a longitudinal study of a chronic fluoxetine treatment in a model of highly emotional mice (BALB/cJ). The function of the 5-HT system in the raphe nuclei and hippocampus, was assessed by using repeated in vivo microdialysis sessions in awake freely moving mice, then studying its relation with behavior, analyzed mainly with open field paradigm. One of the neural mechanisms underlying such delay has been proposed to be the functional status of 5-HT1A autoreceptors in raphe nuclei. Thus, we also assessed the degree of 5-HT1A autoreceptor desensitization by using a local infusion in the raphe of the antagonist, WAY 100635 via reverse microdialysis. We report that the anxiolytic-like effects of fluoxetine correlate in time and amplitude with 5-HT1A autoreceptor desensitization, but neither with the extracellular levels of 5-HT in the raphe nuclei, nor in the hippocampus. Our study suggests that the beneficial anxiolytic/antidepressant-like effects of chronic SSRI treatment indeed depend on 5-HT1A autoreceptor internalization, but do not require a sustained increase in extracellular 5-HT levels in a territory of 5-HT projection such as hippocampus.