BACKGROUND: Status of autonomic homoeostasis in hemostasic disturbances due to hemophilia needs to be studied. OBJECTIVES: To compare autonomic nervous system markers measured by heart rate variability (HRV) and blood flow variability (BFV) in hemophiliacs and healthy age-matched control population using medical analyzer system. DESIGN: Cross-sectional study. SETTINGS: Motiwala Homoeopathy Medical College, and Hemophilia Clinics, Nashik. SUBJECTS: Eighty subjects. INTERVENTIONS: Nil. OUTCOME MEASURES: Autonomic function markers for HRV and BFV. RESULTS: Among 80 subjects, BFV time domain measure, root mean square of successive NN (normal-to-normal) interval differences (RMSSD), was significantly higher among hemophiliacs than nonhemophiliacs. Frequency domain analysis parameter, low frequency for both HRV and BFV was significantly higher among hemophiliacs as compared with nonhemophiliacs. CONCLUSIONS: Hemophiliacs were shown to have higher autonomic activity as compared with healthy controls. Homoeopathic medicines used as an adjunct was associated with decrease in parasympathetic modulations.