BACKGROUND: White blood cells count (WBCc) is a bedrock in the estimation of malaria parasite density in malaria field trials, interventions and patient management. White blood cells are indirectly and relatively used in microscopy to estimate the density of malaria parasite infections. Due to frequent lack of facilities in some malaria-endemic countries, in order to quantify WBCc of patients, an assumed WBCc of 8.0 X 10(9)/L has been set by the World Health Organization to help in estimating malaria parasite densities. METHODS: This comparative analysis study, in Central Ghana, compiled laboratory data of 5,902 Plasmodium falciparum malaria parasite positive samples. Samples were obtained from consented participants of age groups less than five years. Full blood counts (FBC) of participants' samples were analysed using the ABX Micros 60 Haematology Analyzer. Blood slides were read by two competent microscopists to produce concordant results. All internal and external quality control measures were carried out appropriately. Parasite densities were calculated using participants' absolute WBCc and assumed WBCc of 5,000 to 10,000 per microlitre of blood. RESULTS: From the 5,902 Pf malaria positive samples, the mean (SD) WBCc and geometric mean parasite density were 10.4 (4.6) × 10(9)/L and 7,557/μL (95% CI 7,144/μL to 7,994/μL) respectively. The difference in the geometric mean parasite densities calculated using absolute WBCs and compared to densities with assumed WBCs counts were significantly lower for 5.0 × 10(9)/L; 3,937/μL, 6.0 × 10(9)/L; 4,725/μL and 8.0 × 10(9)/L; 6,300/μL. However, the difference in geometric mean parasite density, 7,874/μL (95 % CI, 7,445/μL to 8,328/μL), with assumed WBCc of 10.0 × 10(9)/L was not significant. CONCLUSION: Using the assumed WBCc of 8.0 X 10(9)/L or lower to estimate malaria parasite densities in Pf infected children less than five years old could result in significant underestimation of parasite burden. Assumed WBCc of 10.0 × 10(9)/L at 95 % CI of geometric mean of parasite density statistically agreed with the parasite densities produce by the absolute WBCc of participants. The study suggests where resources are limited, use of assumed WBCc of 10.0 × 10(9)/L of blood to estimate malaria parasite density in central Ghana. Preferably, absolute WBCc should be used in drug efficacy and vaccine trials.