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Differences in the uptake and time to initiation of highly active antiretroviral therapy (HAART), the virological response to HAART, and survival from AIDS by transmission category were analyzed. A multicenter hospital-based cohort of HIV-infected patients attending 10 hospitals in Spain from January 1997 to December 2003 was used. Cross-checks with the National AIDS Registry were performed. Cox proportional hazard models were used to assess the impact of transmission category on time to HAART initiation, viral suppression (defined by first HIV-1 RNA viral load measurement <500 copies/ml after HAART), and survival from AIDS. Of 4643 patients, 73% were men and 56% were injecting drug users (IDUs). A statistically significant interaction was found between transmission category and previous non-HAART antiretroviral treatment (ART) (p < 0.05). Among ART naive patients, IDUs had a 33% lower risk of initiating HAART compared to men who have sex with men (MSM) [HR 0.67 (95% CI 0.57–0.79)]. No differences by transmission categories were seen among patients with prior non-HAART ART. IDUs had poorer viral load (VL) suppression than MSM [HR 0.86 (95% CI 0.74–0.99)] adjusting by baseline VL, AIDS diagnosis, and prior ART. Mortality from AIDS was two and a half times higher in IDUs than MSM [HR 2.51 (95% CI 1.03–6.1)]. Among patients who access the hospital network, IDUs have a lower uptake of HAART, have worse virological suppression, and have higher mortality after AIDS diagnosis. There is a need to extend the programs in order to enhance access and adherence of IDUs to HAART and consider the treatment of drug addiction as an integral part of the treatment for HIV infection.