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Obstructive sleep apnea hypopnea syndrome (OSAHS) is associated with increased risk of cerebrovascular disease. The aim of the present study was to investigate the association between the presence of the small vessel disease (SVD) of the brain in patients with OSAHS. The study included 24 patients with moderate to severe OSAHS and 34 healthy volunteers. All the subjects underwent magnetic resonance imaging (MRI) of the brain, in order to sought periventricular white matter (PVWM), deep white matter (DWM) and brainstem SVD. Among patients with OSAHS, 79.1% had SVD (grade 1–3, Fazekas score) in DWM and 91.7% in PVWM while 22.4% had brainstem—white matter hyperintensities (B-WMH). Patients with OSAHS had a much higher degree of SVD in the DWM and PVWM compared to the control group (<i>p</i> < 0.001). The multivariate analysis showed an independent significant association of OSAHS with SVD (DWM and PVWM) (<i>p</i> = 0.033, OR 95% CI: 8.66 (1.19–63.08) and: <i>p</i> = 0.002, OR 95% CI: 104.98 (5.15–2141)). The same analysis showed a moderate association of OSAHS with B-WMH (<i>p</i> = 0.050, OR 15.07 (0.97–234.65)). Our study demonstrated an independent significant association of OSAHS with SVD and a moderate association of OSAHS with B-WMH.