We sought to describe the prevalence, trends and factors associated with late diagnosis of HIV infection between 2001 and 2008 in Catalonia, Spain. Adults over 13 years of age with available CD4 cell counts, who were notified to the Catalonia Voluntary HIV Surveillance System between January 2001 and December 2008, were included in the study. Late presentation for HIV infection was defined as a CD4 cell count <350 cells/μL or with an AIDS-defining condition at presentation. Multivariable logistic regression was used to identify factors independently associated with late diagnosis of HIV. Of the 4651 newly diagnosed HIV-infected individuals with available CD4 counts, 2598 (55.9%) were diagnosed late. The proportion of people with a late diagnosis decreased from 60.4% in 2001 to 50% in 2008, a significant trend (P < 0.001). Older age, male gender, foreign birth, heterosexuality and injecting drug use were independent risk factors for late diagnosis. Strategies to actively promote HIV testing to populations at risk of late diagnosis of HIV or those never attending health systems should be implemented.