Background: Red blood cell polymorphisms i.e. sickle cell trait HbS and G6PD may play a very important role on increasing severity of arbovirus disease in an infected individual. However, few studies have investigated whether such variants in the human population has an impact on susceptibility to arboviral infections. We investigated possible association between red blood polymorphisms, i.e. HbS and G6PD and arbovirus diseases, dengue and chikungunya in three sites located in north eastern Tanzania. Methods: We use archived samples collected in a large project on an on-going study in June 2013 at Bondo and Hai, and November 2013 Lower Moshi. Prevalence of dengue and chikungunya was detected using IgM and IgG antibodies capture ELISA. Genotyping for HbS and G6PD were performed by high throughput PCR, and then completed by SSOP-ELISA. Results: Compare within the three sites, the prevalence of variant HbS and G6PD was significant higher in Lower Moshi (p<0.001) and (p=0.003) respectively. Conclusion: Our data show that, there is presence of chikungunya and dengue infection in north eastern Tanzania and there is association between HbS and DENV IgM and IgG Key words: red blood cell polymorphisms, glucose 6 phosphate dehydrogenase deficiency, prevalence of arboviruses, sickle cell, dengue, chikungunya, Tanzania