Associations of two alleles of the bovine major histocompatibility complex DRB3 gene (BoLA-DRB3) with lowered somatic cell score (SCS) and occurrence of disease (BoLA-DRB3.2* 16 and *23, respectively) have previously been documented. The objective of this study was to evaluate potential relationships between BoLA-DRB3 alleles with production traits, namely 305-day milk, milk fat and milk protein yield, in a population of Canadian dairy cattle (Holstein, n = 835 and Jersey, n = 66) over the course of two lactations. No significant associations were detected between BoLA alleles and production traits in Jerseys. In Holsteins, alleles *16 and *23 also did not show associations with production traits but allele *8 was significantly associated with increased 305-day milk, fat and protein yields in the previous lactation (the lactation prior to immunization with a gram negative core antigen vaccine), and with increased protein production in the subsequent (with reference to the time of immunization) lactation. Allele *22 was associated with decreased milk and protein yield in both previous and subsequent lactations. Therefore, it can be concluded that increasing or decreasing the frequency of BoLA alleles *16 and *23 to reduce SCS or increase resistance to mastitis in this population would not have adverse effects on production in this population, and that certain BoLA alleles (*8 and *22) are associated with altered production traits in Canadian Holsteins.