Introduction Transcranial Doppler is a method that enables the assessment of different cerebral hemodynamic parameters. It also allows for the evaluation of the presence of right-to-left circulation shunts (RLS) and for the detection of microembolic signals (MESs), which might be associated with an increased risk of cerebrovascular events. For instance, the presence of MESs on transcranial Doppler in patients with systemic lupus erythematous (SLE) and antiphospholipid syndrome (APS) is associated with an increased risk of stroke. Therefore, transcranial Doppler could be a useful tool for stroke risk stratification in these patients. Objective Our objective was to evaluate transcranial Doppler cerebral mean blood flow velocities as well as the presence of MESs and RLS in patients with antiphospholipid syndrome and SLE. Patients and methods Twenty-two patients with primary APS (PAPS), 24 patients with secondary APS (SAPS), 27 patients with SLE without APS and 21 healthy controls were evaluated. Clinical and epidemiological data were compiled from medical charts, and all subjects underwent transcranial Doppler examination with breath-holding index calculation. Both middle cerebral arteries were monitored for 60 min for the detection of MESs. RLS was investigated with agitated saline injected as a bolus. Results There were no significant differences in mean blood flow velocities among the groups. MESs were more frequently found in patients with SLE when compared with controls and patients with APS (SLE: 17.4%, SAPS: 4.3%, PAPS: 0%, controls: 0%, p = 0.03). Anticoagulant therapy was more frequently used in the APS group (PAPS: 81.8%, SAPS: 75.2%, SLE: 1.7%, p < 0.001). Patients with APS had a higher frequency of RLS when compared with volunteers (63.6% versus 38.1%, p = 0.05). Breath-holding index values tended to be lower in patients with SAPS than in control subjects and patients with PAPS and SLE ( p = 0.06). Conclusions Patients with APS had a higher frequency of RLS than healthy controls. This finding alerts to the importance of cardiac investigation in patients with stroke and APS, because further therapies such as RLS occlusion might eventually add protection. The higher frequency of MES in patients with SLE could suggest an effect of anticoagulant therapy on MES prevention, more frequently used in patients with APS.