Background: The majority of patients with hypertrophic cardiomyopathy (HCM) are not disabled by their symptoms; yet HCM is associated with an appreciable incidence of sudden death between 2 % and 4 % annually.Objective: To determine the role of various arrhythmia markers e.g. 24-hour Holter monitoring, ambulatory signal averaged electrocardiogram (SAECG) for detection of late potentials (LPs), 24-hour heart rate variability (HRV) and manual QT analysis (QT dispersion) that help to risk-stratify patients with HCM.Study Population: Twenty consecutive patients with HCH of mean age 28 + 15 years, 14 males 970%) and 6 females (30%) were included in the present study compared with 20 age and sex matched normal control population.Method: All the study groups were subjected to clinical assessment, twelve leads ECG, 24-hour Holter monitoring, including HRV time domain analysis, SAECG and manual QTd.Results: An abnormal SAECG was present in 8 (40%) of the patients versus only 1 (5%) of the normal subjects (P < 0.002). The sensitivity of SAECG in HCM for detection of non-sustained VT is 50%, where specificity 62.5 %, +ve predictive value 25 % and – ve predictive value 83.5 %. Apart from SDANNI the other five time domain HRV indices (mean RR, SDNN, SDNNI, RMSSD and PNN50%) all were significantly reduced in patients with HCM compared to the normal control group. There was no rerlation between HRV time domain indices and clinical variables in patients with HCM except for SDNNI which was significantly lower in patients with non-sustained VT (P = 0.02), PNN 50% was reduced in those with family history of SCD (P = 0.05). QTd and QTcd were significantly longer in patients compared to the control, also significantly longer in patients with non-sustained VT (P = 0.001 and 0.02 respectively). Conclusion: Electrical instability measures were significantly abnormal in HCM patients compared to normal age and sex matched control population, yet they were not correlated with high risk subgroup e.g. family history of SCD, history of syncope, non-sustained VT during Holter monitoring and LVOT pressure gradient.