Introduction: Low adherence to prescribed medication in patients with non communicable diseases (NCDs) increases risk of hospitalization and premature mortality. Assessing adherence to medications and its correlates among NCD patients can help in delivering targeted interventions. Objectives: To assess the level of low adherence to prescribed medications and associated factors among diabetic and/or hypertensive patients registered in NCD clinic at a Rural Health Center in South India. Methodology: A facility based cross-sectional study was conducted in a RHC of Puducherry, India. All the patients who registered and attended clinic for follow up in August 2014, with either hypertension and/or diabetes and received drug for more than four weeks prior to contact were included in study and adherence was assessed using Morisky Medication Adherence Scale (MMAS-8) questionnaire. The data was entered in Microsoft Excel and was analyzed using SPSS version 20. Results: Of the 281 included in the study the mean (SD) age was 57.4 (11.9) years and 169 (59.8%) were females. Among these 281, 155 (55.1%) had only hypertension, 46 (16.4%) had only diabetes and 90 (28.5%) had both hypertension and diabetes. Low adherence to medication was seen in 47 (16.7%) participants. In the model factors like education of 1-5years (OR-2.68, CI-1.03__ampersandsignndash;6.98)), education of __ampersandsigngt;6 years (OR-3.50, CI-1.34__ampersandsignndash;9.14), having only diabetes (OR-3.78, CI-1.28-11.17) and tobacco use (3.51, CI-1.24__ampersandsignndash;9.96) were independently associated with low adherence. Conclusion: Around one-sixth of the patients with either diabetes and/or hypertension were found to be less adherent to prescribed medication. Higher education levels, use of tobacco and having only diabetes were identified independently as risk factors for low adherence.