Introduction: Despite an increasing recognition of non- communicable diseases (NCDs) in sub-Saharan Africa, there is lack of well established surveillance systems for these diseases. In an effort to understand burden of NCDs in low-resource settings, the African Field Epidemiology Network launched a pilot project in 2009 to routinely capture patient data in the diabetes clinic of Mbarara Regional Referral Hospital. The objective of this study was to determine the prevalence and, the gender- and age- specific distributions of common NCD risk factors among diabetic patients attending a referral hospital in rural Uganda. Methods: A relational Access database was designed to collect information on NCD risk factors. These included smoking, alcohol use, family history of diabetes, hypertension and body mass index. Univariate analyses were done and differences in proportions tested using chi-square P-values in STATA version 10.0. Results: A total of 1,383 patient records were analyzed, with 61% being female and mean age of 39.6 years (SD 15.8). About 24% had a family history of diabetes. Smoking and alcohol use were more prevalent among males (16.6 % vs. 8.3%; p<0.0001) and (30.7 vs. 13%; p<0.0001) respectively. Overweight, obesity and hypertension were more prevalent in women (18.6% vs. 9.7%, 8.6% vs. 2.6%; p<0.0001, and 40.3% vs. 33%, p=0.018) respectively. Conclusion: This pilot project shows that use of hospital-based data is a valuable initial step in setting up surveillance systems for NCDs in Uganda. Risk factors for NCDs were both age and gender-specific and predominantly related to lifestyle. This suggests the need to design gender-sensitive prevention interventions that target lifestyle modification in this setting.