SMC proteins are components of cohesin complexes that function in chromosome cohesion. We determined that SMC1alpha and SMC3 localized to wild-type mouse meiotic chromosomes, but with distinct differences in their patterns. Anti-SMC3 coincided with axial elements of the synaptonemal complex, while SMC1alpha was observed mainly in regions where homologues were synapsed. This pattern was especially visible in pachytene sex vesicles where SMC1alpha localized only weakly to the asynapsed regions. At diplotene, SMC3, but not SMC1alpha, remained bound along axial elements of desynapsed chromosomes. SMC1alpha and SMC3 were also found to localize along meiotic chromosome cores of Spo11 null spermatocytes, in which double-strand break formation required for DNA recombination and homologous pairing were disrupted. In Spo11 -/- cells, SMC1alpha localization differed from SMC3 again, confirming that SMC1alpha is mainly associated with homologous or non-homologous synapsed regions, whereas SMC3 localized throughout the chromosomes. Our results suggest that the two cohesin proteins may not always be associated in a dimer and may function as separate complexes in mammalian meiosis, with SMC1alpha playing a more specific role in synapsis. In addition, our results indicate that cohesin cores can form independently of double-strand break formation and homologous pairing.