Recent models of visual recognition have suggested that perceptual analysis may start with a parallel extraction of different spatial frequencies (SF), using a preferential coarse-to-fine (low-to-high SF) sequence of processing. A rapid extraction of low spatial frequency (LSF) information may thus provide an initial and crude parsing of the visual scene, subsequently refined by slow but more detailed high spatial frequency (HSF) information. However, the sequence of SF analysis could be flexible, a high-to-low (HtL) being sometimes preferred to a low-to-high (LtH) SF sequence depending on task demands. Furthermore, it has also been suggested that the right vs. left hemisphere might be differentially specialized in LSF vs. HSF analysis, respectively. By manipulating the temporal succession of LSF and HSF stimuli, the present fMRI study investigated whether such hemispheric specialization may underlie the flexible use of different time-course in SF analysis. Participants performed a matching task between two successive images of natural scenes (LSF or HSF) that were displayed either in an LtH (LSF scene presented first and HSF scene second) or in a reverse HtL sequence. A direct inter-hemispheric comparison of the neural responses evoked by each SF sequence revealed greater activations within the right occipito-temporal cortex for the LtH sequence and within the left occipito-temporal cortex for the HtL sequence. These fMRI results suggest that the hemisphere preferentially engaged during the sequential processing of different SF might be determined by the initial SF-band appearing in this sequence, and that both a coarse-to-fine and fine-to-coarse analysis might independently take place in the two hemispheres.