Background: Depression is a common health condition affecting up to a third of patients attending primary care, where most of the care for people with depression is provided. Adequate recognition of depression is the critical step in the path to effective care, particularly in low income countries. As part of the Programme for Improving Mental healthcare (PRIME), a project supporting the implementation of integrated mental healthcare in primary care, we evaluated the level of recognition of depression by clinicians working in primary care in rural Ethiopia prior to in service training. We hypothesised that the detection rate of depression will be under 10% and that detection would be affected by gender, education and severity of depression. Methods: Cross-sectional survey in eight health centres serving a population of over 160,000 people. A validated version of the 9-item patient health questionnaire (PHQ-9) was administered as an indicator of probable depression. In addition, primary care clinicians completed a clinician encounter form. Participants were consecutive primary care attendees aged 18 years and above. Results: A total of 1014 participants were assessed. Primary care clinicians diagnosed 13 attendees (1.3%) with depression. The PHQ9 prevalence of depression at a cut-off score of ten was 11.5% (n = 117), of whom 5% (n = 6/117) had received a diagnosis of depression by primary care clinicians. Attendees with higher PHQ scores and suicidality were significantly more likely to receive a diagnosis of depression by clinicians. Women (n = 9/13) and participants with higher educational attainment were more likely to be diagnosed with depression, albeit non-significantly. All cases diagnosed with depression by the clinicians had presented with psychological symptoms. Conclusion: Although not based on a gold standard diagnosis, over 98% of cases with PHQ-9 depression were undetected. Failure of recognition of depression may pose a serious threat to the scale up of mental healthcare in low income countries. Addressing this threat should be an urgent priority, and requires a better understanding of the nature of depression and its presentation in rural low-income primary care settings.