BACKGROUND: Past studies have found a relationship between detectable HIV viral load and non-communicable diseases (NCDs) in HIV-infected individuals on antiretroviral therapy in high-income settings, however there is little research in South Africa. Our objective was to investigate the association between detectable HIV viral load and prevalent NCDs in a primary health centre in peri-urban South Africa. METHODS: HIV-infected adults (aged ≥25) who had been on antiretroviral therapy for ≥ six months and attended the HIV clinic within a primary health centre in Khayelitsha, Cape Town, were recruited. We recorded participants' demographics, HIV characteristics, the presence of NCDs via self-report, from clinic folders and from measurement of their blood pressure on the day of interview. We used logistic regression to estimate the association between a detectable HIV viral load and NCD comorbidity. RESULTS: We recruited 330 adults. We found no association between a detectable HIV viral load and NCD comorbidity. Within our multivariable model, female gender (OR3·26; p = 0·02) age > 35 (OR 0·40; p = 0·02) low CD4 count (compared to CD4 < 300 (reference category): CD4:300-449 OR 0·28; CD4:450-599 OR 0·12, CD4:≥600 OR 0·12; p = < 0·001), and ever smoking (OR 3·95; p = < 0·001) were associated with a detectable HIV viral load. We found a lower prevalence of non-communicable disease in clinic folders than was self-reported. Furthermore the prevalence of hypertension measured on the day of interview was greater than that reported on self-report or in the clinic folders. CONCLUSIONS: The lack of association between detectable viral load and NCDs in this setting is consistent with previous investigation in South Africa but differs from studies in high-income countries. Lower NCD prevalence in clinic records than self-report and a higher level of hypertension on the day than self-reported or recorded in clinic folders suggest under-diagnosis of NCDs in this population. This potential under-detection of NCDs may differ from a high-income setting and have contributed to our finding of a null association. Our findings also highlight the importance of the integration of HIV and primary care systems to facilitate routine monitoring for non-communicable diseases in HIV-infected patients.