A total of 1055 nucleotide sequences obtained from HIV patients diagnosed in 2008 and 2009 in Belgium were included in this prevalence study. The study population is a group of patients whose visit was considered by the clinician as the first contact with a Belgian AIDS reference centre or with another clinical centre experienced in HIV care. Prevalences of surveillance drug resistance mutations (SDRM) of 11.7% (47/394) and 11.0% (73/661) were observed in 2008 and 2009, respectively. The highest level of SDRM was observed towards nucleoside reverse transcriptase inhibitors (NRTIs) (7.8%), followed by the non-nucleoside reverse transcriptase inhibitors (NNRTIs) (4.2%) and Protease inhibitors (PIs) (2.3%). A potential clinical impact of the SDRM was demonstrated when using the current first-line therapy. A particularly high prevalence of SDRM was observed among intravenous drug users (IDUs) (29,4%). Reanalysis and comparing the data from previous Belgian studies using similar interpretation algorithms could not reveal a significant trend in SDRM prevalence over the last 5 years.