The geographical location and medical facility may affect the pattern of antihypertensive prescriptions. Information regarding the correlation between the prescription and health care faculties in different geographical locations was lacking.The aim of this study was to compare differences in the prescribing of antihypertensives between hospital-based clinics (hospital arm) and office-based clinics (office arm) in different geographical locations in Taiwan.We collected data from the National Health Insurance database of Taiwan to carry out a population-based, retrospective cohort analysis of 3,218,794 patients newly diagnosed with hypertension in the period January 1, 1997 to December 31, 2004. Eligible participants were classified into either of two groups based on the level of health care faculty: hospital arm and office arm. The covariates composed of age, gender, antihypertensive regimens, urbanization status, comorbidity, and Charlson comorbidity index.There were 2,028,784 cases (63.0 %) for the hospital arm and 1,190,010 (37 %) for the office arm. In the hospital-based arm, there were 168,933 (8.3 %) patients diagnosed with diabetes mellitus, 166,110 (8.2 %) patients diagnosed with coronary artery disease, 147,465 (7.3 %) patients diagnosed with cerebrovascular accident, 86,866 (4.3 %) patients diagnosed with chronic kidney disease, 74,525 (3.7 %) patients diagnosed with benign prostatic hyperplasia, 55,517 (2.7 %) patients diagnosed with congestive heart failure. The all comorbidities in the hospital arm had significantly higher proportions than those in the office arm (p < 0.001). The Charlson comorbidity index in the hospital arm was higher than that in the office arm (p < 0.001). Physicians who practiced in the office arm prescribed polytherapy less often than those in the hospital arm (OR = 0.68, 95 % CI: 0.67-0.68). For overall urbanization status, the adjusted OR of polytherapy prescriptions in the aging city (OR = 1.08, 95 % CI: 1.05-1.12) was higher than other type cities. The highest urbanization-specific OR of polytherapy prescriptions was observed for highly urbanized city in the hospital arm (OR = 1.20, 95 % CI: 1.18-1.23) and aging city in the office arm (OR = 1.42, 95 % CI: 1.21-1.67). In the both arm, patients with lower CCI showed decreased risk of polytherapy prescription.The antihypertensive prescriptions in the clinical practices were different between the hospital arm and the office arm in the different health care, comorbidity, and urbanization status. During the study period, the proportion of antihypertensive polytherapy had declined.