The initial control of viral replication during primary HIV-1 infection is dominated by CD8+ T-cell mediated responses. Neutralizing IgG to autologous virus is first detected in serum weeks after this response when the viraemia has already declined. However, the mucosal and systemic HIV-1 neutralizing IgA response during primary HIV-1 infection in patients treated with HAART has not been studied previously. The presence of HIV-1 neutralizing IgA antibodies in serum (n=10 patients) and semen (n=6 patients) samples was tested against a laboratory adapted HIV-1 isolate and against primary HIV-1 isolates, representing different clades and phenotypes. The patients received HAART during the study period and were followed from primary HIV-1 infection and up to 72 weeks. Overall, HIV-1 neutralizing IgA activity could be demonstrated in serum from 5 of 10 primary HIV-1 infected patients at inclusion, although the response was restricted to only 1 of the 4 tested isolates. In semen samples, HIV-1 neutralizing IgA activity was seen in 2 of 5 patients against at least 1 of the HIV-1 isolates. In conclusion, a restricted but early neutralizing IgA response can be detected in serum and semen in primary infected patients treated with HAART.