The rapid introduction of non-B HIV-1 subtypes into Quebec, mostly from persons from regions where HIV prevalence is high and where different variants circulate, means that recombination must now be an important consideration in the epidemiologic surveillance of HIV infection. No circulating recombinant form (CRF), currently involving exclusively subtypes A1 and C, exists in the Los Alamos HIV database. This study presents a near full-length genomic analysis of a novel HIV-1 recombinant involving subtypes A1 and C. Bootscanning revealed that the recombinant structure involves three breakpoints that separate the genome into four regions, alternating between subtypes A1 and C. The intersubtype recombinant breakpoint in the pol gene was at midpoint between the protease and reverse transcriptase open reading frames. This is the first report of a recombinant involving subtypes A1 and C in Canada, the epidemiologic significance of which is not yet known.