OBJECTIVE: In six United Nations Relief and Works Agency (UNRWA) primary health care clinics in Jordan serving Palestine refugees diagnosed with hypertension, to determine the number, characteristics, programme outcomes and measures of disease control for those registered up to 30 June, 2013, and in those who attended clinic in the second quarter of 2013, the prevalence of disease-related complications between those with hypertension only and hypertension combined with diabetes mellitus. METHOD: Retrospective cohort study with programme and outcome data collected and analysed using E-Health. RESULTS: There were 18 881 patients registered with hypertension with females (64%) and persons aged ≥ 40 years (87%) predominating. At baseline, cigarette smoking was recorded in 17%, physical inactivity in 48% and obesity in 71% of patients. 77% of all registered patients attended clinic in the second quarter of 2013; of these, 50% had hypertension and diabetes and 50% had hypertension alone; 9% did not attend the clinics and 10% were lost to follow-up. Amongst those attending clinic, 92% had their blood pressure measured, of whom 83% had blood pressure <140/90 mm Hg. There were significantly more patients with hypertension and diabetes (N = 966, 13%) who had disease-related complications than patients who had hypertension alone (N = 472, 6%) [OR 2.2, 95% CI 2.0-2.5], and these differences were found for both males [18% vs. 10%, OR 1.9, 95% CI 1.6-2.2] and females [11% vs. 5%, OR 2.4, 95% CI 2.1-2.9]. CONCLUSION: Large numbers of Palestine refugees are being registered and treated for hypertension in UNRWA primary health care clinics in Jordan. Cohort analysis and E-Health can be used to regularly assess caseload, programme outcomes, clinic performance, blood pressure control and cumulative prevalence of disease-related complications. Current challenges include the need to increase clinic attendance and attain better control of blood pressure.