Background: It is known that dynamic cerebral autoregulation (dCA) is acutely impaired following ischaemic stroke (IS). However, the influence of stroke subtype, the affected (AF) and unaffected (UA) hemispheres, and the effects of a methodological approach on dCA estimates in stroke are all inconclusive. Therefore, we studied cortical and subcortical acute IS (AIS) patients to test the primary hypotheses that (1) dCA is impaired in stroke subtypes when compared to controls, (2) dCA impairment is more pronounced in the AF compared with the UA hemisphere, and (3) similar results are obtained with both spontaneous blood pressure (BP) fluctuation techniques, and sudden induced BP changes by thigh cuff deflation. Methods: We assessed the dCA values in AIS patients and in healthy controls (n = 10). The AIS patient group consisted of anterior circulation cortical (n = 11) and subcortical (n = 11) strokes within 48 h of symptom onset. Cerebral blood flow velocity was measured using transcranial Doppler ultrasound, and BP measurements were recorded before, during and after the release of bilateral thigh cuffs in 10 controls (7 males) of a mean age of 59 ±15 years (range 31-75), 11 cortical strokes (7 males) of a mean of age 65 ± 19 years (range 25-88) and 11 subcortical strokes (7 males) of a mean age of 60 ± 18 years (range 39-85). Autoregulation index (ARI) estimates, calculated using spontaneous fluctuations and thigh cuff manoeuvre, were derived. Differences in ARI (Tiecks' model) were tested with repeated-measures ANOVA. Results: A total of 22 patients were included, comprising 11 subcortical (lacunar clinical syndrome) and 11 cortical strokes (total anterior circulation stroke/partial anterior circulation syndrome). Of the 10 control subjects, 1 later withdrew because of intolerance to the thigh cuffs. Similar ARI estimates were obtained in both groups, whether assessed from spontaneous fluctuations or thigh cuff measurements (p = 0.37). ARI differences were not significantly different between hemispheres for both control and stroke populations. ARI was significantly impaired in AIS patients compared to age-, sex- and BP-matched control subjects, with a greater impairment of dCA observed in cortical IS. Conclusions: The results of this study suggest that both spontaneous fluctuations and thigh cuff deflation techniques are able to provide reliable estimates of ARI, with the estimates from both spontaneous fluctuations and thigh cuff deflation techniques being in keeping with those reported elsewhere in the literature. dCA was impaired following AIS compared to controls when stroke subtype was considered. Importantly, no differences were observed between UA and AF. This has implications for the assessment of CA after stroke and reinforces the need to define a ‘gold standard' test for the investigation of CA.