Purpose Detection of end-organ damage (EOD) in systemic hypertension is essential for the management of systemic hypertension. We aimed to evaluate subfoveal choroidal thickness (SFCT) and retinal layers' thicknesses by using spectral domain optical coherence tomography (SD-OCT) in patients with systemic hypertension and to assess the relationship between EOD and SD-OCT parameters. Methods A total of 189 consecutive patients with systemic hypertension and 100 controls were included. Patients were examined to detect EOD including hypertensive retinopathy (HTRP), left ventricular hypertrophy assessed by transthoracic echocardiography and microalbuminuria assessed by 24-h urine analysis. SFCT, inner plexiform-ganglion cell complex (IP-GCC), peripapillary retinal nerve fiber layer (pRNFL) and central macular thickness (CMT) were measured with SD-OCT. Results Patients with systemic hypertension had significantly lower SFCT and retinal layer thicknesses than controls (P<0.001). In the dilated fundus photographic evaluation, 94 patients with systemic hypertension had HTRP and these patients had lower SFCT, CMT, IP-GCC and pRNFL thicknesses compared to hypertensive patients without HTRP and healthy controls. Patients with EOD had significantly lower SFCT, CMT, IP-GCC and pRNFL thicknesses and as the number of EOD increased, the SFCT decreased significantly. In the multivariate analysis, SFCT was found as an independent predictor of EOD (P<0.001, odds ratio: 0.0605). Conclusion Hypertensive patients, especially with EOD had significantly lower SD-OCT parameters compared to controls. It would be rational to add SD-OCT assessment to conventional hypertensive retinopathy evaluation in patients with systemic hypertension for early diagnosis of end-organ damage, burden of target organ involvement and monitoring anti-hypertensive treatment.