This study aimed to investigate any cerebral function deficits in AS using functional MRI technology and its possible relationship to clinical and laboratory results. Twenty seven patients with AS and 28 control subjects were included in this study. All of them underwent structural MRI and resting state-functional MRI (rs-fMRI) scanning. Comparisons of amplitude of low frequency fluctuations (ALFF) of rs-fMRI signals between AS patients and normal controls were performed using two sample t-tests. To examine functional connectivity within the groups, one-sample t tests were performed on the individual z-value maps. The z values were compared between the two groups using two-sample t test. Partial correlations between ALFF values and functional connectivity of the brain regions which showed group difference and clinical results including the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) score, the serum high-sensitivity C-reactive protein (hsCRP), and the erythrocyte sedimentation rate (ESR) were analyzed for AS patients.Compared with normal controls, the AS patients exhibited significant lower ALFF in the left medial frontal gyrus, the right precentral gyrus and the right posterior cingulate, while higher ALFF in the left cerebellum anterior lobe, the left middle temporal gyrus, the left superior occipital gyrus, the left postcentral gyrus and the right precuneus. AS patients showed widespread brain connectivity alterations. Functional connectivity strength of the left precuneus and the left middle temporal gyrus were closely correlated with the the BASDAI scores, ESR and hsCRP in AS patients. AS is the most common clinical subgroup of seronegative spondyloarthropathies. Neurological impairment in the course of AS is very important. Early diagnosis and detection of it may stop the progress of neurological complications and improve the quality of patients’ lives greatly . Recent years, somatosensory evoked potential (SSEP) and magnetic motor evoked potentials (MEP) have been proved useful to detect neurological complications of AS [6, 7]. However, cortical morphology and functional alterations related with this disease have not been reported in the literature. This is the first study to investigate AS-related cortical activity changes using resting state fMRI. Compared to controls, AS patients exhibited significant lower ALFF in the left medial frontal gyrus, the right precentral gyrus and the right posterior cingulate. These findings suggest that the brain regions described above may be the most affected areas in AS. The altered spontaneous ALFF values in these area are possible characteristic of neurological impairments. In this study we also found higher ALFF in several brain regions especially the left cerebellum anterior lobe. The increased activity may be a compensatory reactions that allow increased recruitment of neurons. In this study we found AS patients showed widespread brain connectivity alterations and connectivity strength of the left precuneus and the left middle temporal gyrus were closely correlated with the BASDA scores, ESR and hsCRP. Our findings suggest that connectivity strength of the left middle temporal gyrus and left precuneus could reflect clinical manifest and laboratory results of AS. R-fMRI may be a helpful tool in the imaging development of AS diagnosis and evaluation. The precise mechanisms leading to the connectivity alteration in AS are not understood. An association between AS and multiple sclerosis has been proved, possibly due to an immunological defect. The demyelination is common in multiple sclerosis, which can disrupt the interactions among different brain regions and lead to network disruption. AS is associated with a altered cortical activity of rs-fMRI signals. Measurement of functional connectivity strength of the left precuneus and the left middle temporal gyrus may aid in the clinical detection and evaluation of AS.