Introduction: Fine needle aspiration (FNA) is frequently the first noninvasive test used for the diagnostic workup of lymphadenopathy. There have been many studies showing its usefulness, especially in conjunction with other techniques for the diagnosis of lymphoma, but it remains inferior to histological examination. The data regarding this subject have mostly been reported mostly from first-world countries, but are scarce for emerging economies. Thus, the current study assesses the agreement between fine needle aspiration flow cytometry (FNA FC) and histology in the aforementioned region. Material and Methods: We conducted a retrospective study including the FNA FC adenopathy diagnoses made between January 2011 and December 2016 at the Tygerberg Hospital, Cape Town, South Africa. Additional variables included were the histological diagnosis, sex and age of the included patients. Results: In the descriptive part of the current study, 269 FNA FC samples were included. The most frequent diagnoses made on these were represented by B-cell lymphoma, reactive adenopathy, no abnormality detected (NAD), and non-hematological malignancy. In the analytical part of the current study, there were 115 cases included that had both valid FNA FC and histological diagnoses. It could be observed that FNA FC can correctly diagnose B-cell lymphoma in most cases, but it is a poor diagnostic tool especially for Hodgkin lymphoma in this setting as only a four-color flow cytometer was available for diagnosis. Moreover, FNA FC diagnosis of reactive adenopathy and of no abnormalities detected was shown to frequently hide a malignant disease. Conclusion: In countries with scarce resources, FNA FC represents a useful diagnostic tool in the case of B-cell lymphoma, but may misdiagnose reactive adenopathy. Thus, FNA FC should be used in a case-specific manner, in addition to as a screening tool, with the knowledge that in cases with a high clinical suspicion of lymphoma, histological diagnosis is a necessity.