Plasmodium falciparum is a predominant malaria species that infects humans in the African continent. A recent WHO report estimated 95% and 5% of P. falciparum and P. vivax malaria cases, respectively, in Sudan. However many laboratory reports from different areas in Sudan indicated otherwise. In order to verify, we selected four hundred suspected malaria cases from Aljabalain area located in the White Nile state, central Sudan, and diagnosed them with quality insured microscopy and species-specific nested PCR. Our results indicated that the proportion of P. vivax infections among suspected malaria cases was high. We found that on average 20% and 36.5% of malaria infections in both study areas were caused by P. vivax using both microscopy and PCR, respectively. This change in pattern is likely due to the recent demographic changes and high rate of immigration from neighbouring countries in the recent years. This is the first extensive clinical study of its kind that shows rising trend in P. vivax malaria cases in White Nile area, Sudan.