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Human cytomegalovirus (HCMV) is a ubiquitous pathogen with ability to establish a persistent infection in the host for many years. Diseases are more serious in congenitally infected infants and immunocompromised individuals such as AIDS patients and transplant recipients. It rarely causes disease among immunocompetent individuals. The envelope glycoproteins of HCMV (gB, gH, gN, gM, gL and gO) are essential for viral infectivity as they are involved in attachment and penetration of the host cell, cell to cell viral transmission and fusion of infected cells. Also, they are known to be important targets for humoral and cell mediated immune responses against the virus. The hypothesis states that HCMV genotypes are constantly mutating and evolving, then is controlled in a setting of immunocompetence, but in immunocompromised patients, congenitally infected patients or possibly within the CNS, the virus is able to evade the immune system and genotypes may evolve which are more pathogenic and/or neuroinvasive. In current study, a total of 669 CSF samples were collected from Malawian children with neurological illness that have been tested for the presence of HCMV. A comparison study population was also studied which contained 26 HCMV isolates obtained from the Manchester Royal Infirmary Clinical Virology Laboratory. The isolates were originally collected from congenitally CMV infected infants or immunocompromised children and adults showing symptoms of HCMV disease. Positive HCMV samples were screened for glycoproteins (B, H, N, L and O) and then glycotyped by restriction fragment length polymorphisms and sequencing analysis. HCMV DNA was found to be present in 46 (6.7%) out of 669 CSF samples. In 19 of these HCMV positive samples, glycoprotein genotypes (B, H, N, L and O) were identified. The predominant glycoprotein genotypes in the CSF population were as follows, gB type 3(63.2%), gH type 1(73.2%), gN type 4 (50%), gL type 4 (55.8%) and gO type 1 (60%), whilst in the comparison study population (control group) the most common glycoprotein genotypes were; gB type 3 (52.3%), gH type 1 (52%), gN type 4 (60%), gL type 4 (56%) and gO type 1(48%). No statistically significant difference was found between glycoprotein genotypes among the CSF samples and comparison study population. However, when linkage between glycoprotein types was studied and analysed differences between the two populations emerged. The particular glycoprotein linkage (gH1, gN1 and gO1) occured six times in the CSF study population with severe and fatal outcome as it occured four times with fatal outcome, and in two other patients, one was HIV positive and one with sequelae.Novel linkages between gO and gN genotypes were also found (gN3b/gO3), (gN4a/gO4), (gN4b/gO2b), (gN4b/gO3), (gN4d/gO1c), (gN1/gO1c), and (gN4c/gO4). The (gN1/gO1c) combination was occurred three times, but only in CSF study population and was associated with fatal outcomes, two patients died and one was HIV positive patients.RFLP assay was found to have limited efficacy in identification of HCMV genotypes, as discrepancies in genotype results between RFLP and sequencing were found in all glycoprotein genotypes. Thus, sequencing analysis was more accurate and recommended for identification of the HCMV genotypes.In conclusion, investigation of different glycoprotein genotypes in CSF samples has shown no significant correlation between single glycoprotein and disease outcome. Recombination between HCMV strains may lead to progression of disease. However, studying a large group of CSF samples positive for HCMV from immunocompromised patients may clarify the correlation between glycoprotein types and neurological outcome, and lead to improved strategies for treatment and prevention of HCMV associated disease.