Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is widespread across malaria endemic regions. G6PD-deficient individuals are at risk of haemolysis when exposed, among other agents, to primaquine and tafenoquine, which are capable of blocking malaria transmission by killing Plasmodium falciparum gametocytes and preventing Plasmodium vivax relapses by targeting hypnozoites. It is evident that no measures are currently in place to ensure safe delivery of these drugs within the context of G6PDd risk. Thus, determining G6PDd prevalence in malarious areas would contribute towards avoiding possible complications in malaria elimination using the drugs. This study, therefore, was aimed at determining G6PDd prevalence in Gambella hospital, southwest Ethiopia, using CareStart™ G6PDd fluorescence spot test. Venous blood samples were collected from febrile patients (n = 449) attending Gambella hospital in November-December 2013. Malaria was diagnosed using blood films and G6PDd was screened using CareStart™ G6PDd screening test (Access Bio, New Jersey, USA). Haematological parameters were also measured. The association of G6PD phenotype with sex, ethnic group and malaria smear positivity was tested. Malaria prevalence was 59.2% (96.6% of the cases being P. falciparum mono infections). Totally 33 participants (7.3%) were G6PD-deficient with no significant difference between the sexes. The chance of being G6PD-deficient was significantly higher for the native ethnic groups (Anuak and Nuer) compared to the 'highlanders'/settlers (odds ratio (OD) = 3.9, 95% confidence interval (CI) 0.481-31.418 for Anuak vs 'highlanders'; OD = 4.9, 95% CI 0.635-38.00 for Nuer vs 'highlanders'). G6PDd prevalence among the Nuer (14.3%) was significantly higher than that for the Anuak (12.0%). G6PDd prevalence in the area is substantial with 30 (90.9%) of the 33 deficient individuals having malaria suggesting the non-protective role of the disorder at least from clinical malaria. The indigenous Nilotic people tend to have a higher chance of being G6PD-deficient as 32 (96.9%) of the total 33 cases occurred among them.