Gene introgression into allopolyploid crop species from diploid or polyploid ancestors can be accomplished through homologous or homoeologous chromosome pairing during meiosis. We produced trigenomic Brassica interspecific hybrids (genome complements AABC, BBAC and CCAB) from the amphidiploid species Brassica napus (AACC), Brassica juncea (AABB) and Brassica carinata (BBCC) in order to test whether the structure of each genome affects frequencies of homologous and homoeologous (both allosyndetic and autosyndetic) pairing during meiosis. AABC hybrids produced from three genotypes of B. napus were included to assess the genetic control of homoeologous pairing. Multi-colour fluorescent in situ hybridisation was used to quantify homologous pairing (e.g. A-genome bivalents in AABC), allosyndetic associations (e.g. B–C in AABC)and autosyndetic associations (e.g. B–B in AABC) at meiosis. A high percentage of homologous chromosomes formed pairs (97.5–99.3%), although many pairs were also involved in autosyndetic and allosyndetic associations. Allosyndesis was observed most frequently as A–C genome associations (mean 4.0 per cell) and less frequently as A–B genome associations (0.8 per cell) and B–C genome associations (0.3 per cell). Autosyndesis occurred most frequently in the haploid A genome (0.75 A–A per cell) and least frequently in the haploid B genome (0.13 B–B per cell). The frequency of C–C autosyndesis was greater in BBAC hybrids (0.75 per cell) than in any other hybrid. The frequency of A–B, A–C and B–C allosyndesis was affected by the genomic structure of the trigenomic hybrids. Frequency of allosyndesis was also influenced by the genotype of the B. napus paternal parent for the three AABC (B. juncea × B. napus) hybrid types. Homoeologous pairing between the Brassica A, B and C genomes in interspecific hybrids may be influenced by complex interactions between genome structure and allelic composition.